Mercurial > repos > rnateam > dewseq

annotate analyseStudy.Rmd @ 0:e1cb2e012307 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
author rnateam
date Thu, 20 Oct 2022 08:18:30 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
1 ---
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
2 title: "DEWSeq Analysis"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
3 author: "Thomas Schwarzl and Sudeep Sahadevan"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
4 date: "07/10/2020"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
5 output:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
6 BiocStyle::html_document:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
7 toc: true
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
8 toc_float: true
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
9 toc_depth: 5
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
10 params:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
11 protein: ""
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
12 sampleinfo_file: ""
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
13 countmatrix_file: ""
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
14 annotation_file: ""
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
15 output_windows_file: ""
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
16 output_regions_file: ""
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
17 output_bed_file: ""
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
18 output_rdata: ""
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
19 min_count: 2
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
20 min_sample: 2
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
21 LRT: FALSE
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
22 p_value_cutoff: 0.05
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
23 lfc_cutoff: 1
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
24 overlap_correction: FALSE
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
25 IHW: TRUE
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
26 decide_fit: TRUE
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
27 ---
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
28 ```{r setup, include=FALSE}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
29 knitr::opts_chunk$set(echo = TRUE)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
30 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
31
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
32
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
33 ```{r assignData, echo=FALSE, eval=TRUE}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
34 protein <- params$protein
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
35 sampleinfo_file <- params$sampleinfo_file
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
36 countmatrix_file <- params$countmatrix_file
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
37 annotation_file <- params$annotation_file
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
38 output_windows_file <- params$output_windows_file
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
39 output_regions_file <- params$output_regions_file
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
40 output_bed_file <- params$output_bed_file
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
41 output_rdata <- params$output_rdata
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
42 min_count <- params$min_count
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
43 min_sample <- params$min_sample
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
44 p_value_cutoff <- params$p_value_cutoff
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
45 lfc_cutoff <- params$lfc_cutoff
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
46 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
47
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
48 Sanity check input parameter values
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
49
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
50 ```{r sanityCheck, echo=FALSE, eval=TRUE}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
51 # round of min_count and min_sample values first
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
52 message("Any decimals given as values for min_count and min_sample parameters will be rounded off to the nearest integer.")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
53 min_count <- round(min_count)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
54 min_sample <- round(min_sample)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
55 # receive and sanity check p_value_cutoff
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
56 if (p_value_cutoff <= 0 || p_value_cutoff >= 1) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
57 warning("p_value_cutoff must satisfy: 0<=p_value_cutoff<=1. Resetting to default value: 0.05")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
58 p_value_cutoff <- 0.05
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
59 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
60 # sanity check log2Foldchange cutoff
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
61 if (lfc_cutoff < 0) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
62 warning("lfc_cutoff must be a value >=0. Resetting to default value: 1.00")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
63 lfc_cutoff <- 1.0
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
64 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
65 # sanity check LRT vs Wald
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
66 if (is(params$LRT, "logical")) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
67 lrt <- params$LRT
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
68 }else {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
69 warning("LRT must be TRUE or FALSE, setting this parameter to default: FALSE")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
70 lrt <- FALSE
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
71 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
72 # sanity check overlap correction parameter
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
73 if (is(params$overlap_correction, "logical")) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
74 overlap_correction <- params$overlap_correction
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
75 }else {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
76 warning("overlap_correction must be TRUE or FALSE, setting this parameter to default: TRUE")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
77 overlap_correction <- TRUE
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
78 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
79 # sanity check IHW vs BH correction parameter
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
80 if (is(params$IHW, "logical")) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
81 ihw_filt <- params$IHW
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
82 }else {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
83 warning("IHW must be TRUE or FALSE, setting this parameter to default: TRUE")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
84 ihw_filt <- TRUE
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
85 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
86 # sanity check automated fit vs parametric fit paramter
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
87 if (is(params$decide_fit, "logical")) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
88 decide_fit <- params$decide_fit
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
89 }else {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
90 warning("decide_fit must be TRUE or FALSE, setting this parameter to default: TRUE")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
91 decide_fit <- TRUE
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
92 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
93 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
94
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
95 # eCLIP analysis of `r protein`
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
96
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
97
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
98 ## Setup
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
99
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
100 This is the analysis of __`r protein`__ with
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
101 sampleinfo file: ``r sampleinfo_file``
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
102 countmatrix file: ``r countmatrix_file`` and
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
103 annotation file: ``r annotation_file``
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
104
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
105 with the following threshold:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
106
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
107 minimum read count per window per sample: ``r min_count``
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
108 number of samples with minimum read count per window: ``r min_sample``
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
109
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
110 using the following parameters:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
111 p-value cut-off: ``r p_value_cutoff``
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
112 Log2FoldChange cut-off: ``r lfc_cutoff``
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
113 use automated method for dispersion estmation: ``r decide_fit``
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
114 use LRT test : ``r lrt``
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
115 use overlap correction: ``r overlap_correction``
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
116 use IHW for FDR correction: ``r ihw_filt``
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
117
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
118
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
119 ``` {r check if files exists, echo=FALSE}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
120 file_exists <- function(x) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
121 if (!file.exists(x))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
122 stop(paste0("'", x, "' - file does not exist."))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
123 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
124
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
125 file_exists(countmatrix_file)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
126 file_exists(annotation_file)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
127 file_exists(sampleinfo_file)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
128 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
129
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
130 First, we load the libraries.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
131
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
132 ```{r load DEWSeq}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
133 required_packages <- c("DEWSeq", "data.table", "IHW", "R.utils", "tidyverse", "ggrepel")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
134 installed_packages <- installed.packages()[, 1]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
135 missing_packages <- setdiff(required_packages, installed_packages)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
136 if (length(missing_packages) != 0) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
137 stop("Found missing dependencies! Please install the following package(s): ", paste(missing_packages, collapse = ", "))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
138 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
139 suppressPackageStartupMessages({
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
140 require(DEWSeq)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
141 require(tidyverse)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
142 require(data.table)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
143 require(IHW)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
144 require(R.utils)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
145 require(ggrepel)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
146 })
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
147 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
148
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
149 ## Read in data
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
150
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
151 Here we read in the window counts
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
152
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
153 ```{r read window counts}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
154 window_counts <- fread(countmatrix_file, sep = "\t", stringsAsFactors = FALSE) %>% as.data.frame()
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
155 rownames(window_counts) <- window_counts[, 1]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
156 window_counts <- window_counts[, -1]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
157 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
158
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
159 and the sample info file
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
160
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
161 ```{r read sample info}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
162 sample_info <- read.table(sampleinfo_file, sep = "\t", stringsAsFactors = FALSE)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
163 if (ncol(sample_info) < 2) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
164 stop("sampleinfo_file ", sampleinfo_file, " MUST have atleast two columns: first column should be the sample names used in ", countmatrix_file,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
165 " and second column must be the experiment type: IP or SMI")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
166 }else if (ncol(sample_info) > 2) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
167 message("Found ", ncol(sample_info), " columns in ", sampleinfo_file, " using the first column as sample name and second column as experiment name")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
168 sample_info <- sample_info[, c(1, 2)]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
169 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
170 colnames(sample_info) <- c("samples", "type")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
171 rownames(sample_info) <- sample_info[, 1]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
172 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
173
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
174 Now we make sure that the sampleinfo file contains the column "type" with values "SMI" and "IP" only.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
175
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
176 ```{r sampleSanity}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
177 # make sure that sample_info rows and window_counts columns are in same order
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
178 common_samples <- sort(intersect(colnames(window_counts), rownames(sample_info)))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
179 if (length(common_samples) != ncol(window_counts)) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
180 stop("The number of samples in ", countmatrix_file, " and ", sampleinfo_file, " do not MATCH!")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
181 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
182 sample_info <- sample_info[common_samples, ]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
183 window_counts <- window_counts[, common_samples]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
184 # Now make sure that sample_info$type contains only "IP" and "SMI"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
185 type_check <- setdiff(unique(sample_info$type), c("IP", "SMI"))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
186 if (length(type_check) != 0) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
187 stop("The second column in ", sampleinfo_file, " should contain analysis types:'IP' or 'SMI' only. Found unknown value(s): ",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
188 paste(type_check, collapse = ", "))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
189 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
190 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
191
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
192 We make sure that only IP and SMI are in the right factor level order
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
193
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
194 ```{r sampleFactor}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
195 sample_info <- sample_info %>% mutate(type = factor(type, levels = c("SMI", "IP")))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
196 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
197
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
198
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
199
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
200 We create the DEWSeq object
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
201
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
202 ```{r dewseqInit}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
203 ddw <- DESeqDataSetFromSlidingWindows(countData = window_counts,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
204 colData = sample_info,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
205 annotObj = annotation_file,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
206 tidy = FALSE,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
207 design = ~type)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
208 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
209
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
210
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
211 ## Prefiltering
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
212
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
213 ```{r prefiltering1}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
214 # remove all empty windows
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
215 keep <- rowSums(counts(ddw)) >= 1
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
216 ddw <- ddw[keep, ]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
217 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
218
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
219
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
220 ## Estimating size factors
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
221
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
222
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
223 ```{r size factors}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
224 ddw <- estimateSizeFactors(ddw)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
225 sizeFactors(ddw)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
226 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
227
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
228 ### estimate size factors for only protein_coding genes
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
229
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
230 ```{r protein_coding_size_factors}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
231 ddw_mrnas <- ddw[rowData(ddw)[, "gene_type"] == "protein_coding", ]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
232 ddw_mrnas <- estimateSizeFactors(ddw_mrnas)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
233 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
234
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
235 ### estimate size factors without significant windows
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
236
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
237 ```{r size_factors_no_sig_windows}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
238 ddw_tmp <- ddw
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
239 ddw_tmp <- estimateDispersions(ddw_tmp, fitType = "local", quiet = TRUE)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
240 if (lrt) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
241 ddw_tmp <- nbinomLRT(ddw_tmp, full = ~type, reduced = ~1)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
242 }else {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
243 ddw_tmp <- nbinomWaldTest(ddw_tmp)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
244 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
245
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
246 tmp_significant_windows <-
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
247 results(ddw_tmp,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
248 contrast = c("type", "IP", "SMI"),
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
249 tidy = TRUE,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
250 filterFun = ihw) %>%
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
251 dplyr::filter(padj < p_value_cutoff) %>%
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
252 .[["row"]]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
253 rm(ddw_tmp)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
254 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
255
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
256 estimate the size factors without the significant windows.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
257
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
258 ```{r final_size_factors}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
259 ddw_mrnas <- ddw_mrnas[!rownames(ddw_mrnas) %in% tmp_significant_windows, ]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
260 ddw_mrnas <- estimateSizeFactors(ddw_mrnas)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
261 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
262
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
263 before thresholding:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
264 ```{r threshold1}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
265 dim(ddw)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
266 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
267
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
268 Now threshold the windows read count table.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
269 ```{r threshold2}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
270 keep_exp <- which(rowSums(counts(ddw) > min_count) >= min_sample)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
271 ddw <- ddw[keep_exp, ]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
272 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
273
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
274 after thresholding:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
275 ```{r threshold3}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
276 dim(ddw)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
277 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
278 assign size factors
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
279
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
280 ```{r final_assign}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
281 sizeFactors(ddw) <- sizeFactors(ddw_mrnas)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
282 rm(list = c("tmp_significant_windows", "ddw_mrnas"))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
283 sizeFactors(ddw)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
284 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
285
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
286
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
287 ## Differential window analysis
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
288
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
289 ### Dispersion estimates
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
290
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
291 ```{r source, echo = FALSE, eval = FALSE}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
292 # source: https://support.bioconductor.org/p/81094/
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
293 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
294 We fit parametric and local fit, and decide the best fit following this [Bioconductor post](https://support.bioconductor.org/p/81094/)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
295
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
296 ```{r parametric_dispersion}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
297 parametric_ddw <- estimateDispersions(ddw, fitType = "parametric")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
298 if (decide_fit) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
299 local_ddw <- estimateDispersions(ddw, fitType = "local")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
300 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
301
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
302 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
303
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
304 This is the dispersion estimate for parametric fit
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
305 ```{r plot parametric fit, fig.wide=TRUE}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
306 plotDispEsts(parametric_ddw, main = "Parametric fit")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
307 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
308
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
309 This is the dispersion estimate for local fit, given automated decision fitting is enabled:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
310 ```{r plot local fit, fig.wide = TRUE}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
311 if (decide_fit) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
312 plotDispEsts(local_ddw, main = "Local fit")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
313 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
314
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
315 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
316
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
317 This will get the residuals for either fit, only for automated decision fitting
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
318 ```{r residual fit}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
319 parametric_resid <- na.omit(with(mcols(parametric_ddw), abs(log(dispGeneEst) - log(dispFit))))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
320 if (decide_fit) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
321 local_resid <- na.omit(with(mcols(local_ddw), abs(log(dispGeneEst) - log(dispFit))))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
322 resid_df <- data.frame(residuals = c(parametric_resid, local_resid),
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
323 fitType = c(rep("parametric", length(parametric_resid)),
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
324 rep("local", length(local_resid))))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
325 summary(resid_df)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
326 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
327
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
328 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
329
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
330 and we plot histograms of the fits
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
331
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
332 ```{r plot residual histograms, fig.wide = TRUE}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
333 if (decide_fit) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
334 ggplot(resid_df, aes(x = residuals, fill = fitType)) +
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
335 scale_fill_manual(values = c("darkred", "darkblue")) + geom_histogram(alpha = 0.5, position = "identity", bins = 100) +
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
336 theme_bw()
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
337 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
338
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
339 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
340
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
341 Now, we will decide for the better fit based on median
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
342
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
343 ```{r choose_fit}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
344 summary(parametric_resid)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
345 if (decide_fit) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
346 summary(local_resid)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
347 if (median(local_resid) <= median(parametric_resid)) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
348 cat("chosen fitType: local")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
349 ddw <- local_ddw
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
350 }else {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
351 cat("chosen fitType: parametric")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
352 ddw <- parametric_ddw
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
353 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
354 rm(local_ddw, parametric_ddw, resid_df, parametric_resid, local_resid)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
355 }else {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
356 ddw <- parametric_ddw
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
357 rm(parametric_ddw)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
358 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
359
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
360 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
361
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
362
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
363
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
364 ### Wald test or LRT
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
365
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
366 ```{r wald_or_LRT}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
367 if (lrt) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
368 ddw <- nbinomLRT(ddw, full = ~type, reduced = ~1)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
369 }else {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
370 ddw <- nbinomWaldTest(ddw)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
371 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
372
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
373 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
374
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
375
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
376 ### Significance testing
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
377
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
378 ```{r sig_windows}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
379 result_windows <- resultsDEWSeq(ddw,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
380 contrast = c("type", "IP", "SMI"),
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
381 tidy = TRUE) %>% as_tibble
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
382
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
383 result_windows
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
384 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
385
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
386
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
387 ### Multiple hypothesis correction with IHW
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
388
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
389 You might be interested to correct for multiple hypothesis testing with IHW.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
390
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
391 Decide on overlap correction based on the parameter `overlap_correction`
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
392
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
393 ```{r ihw}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
394 if (overlap_correction && ihw_filt) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
395 result_windows[, "p_adj_IHW"] <- adj_pvalues(ihw(pSlidingWindows ~ baseMean,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
396 data = result_windows,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
397 alpha = p_value_cutoff,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
398 nfolds = 10))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
399 padj_col <- "p_adj_IHW"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
400 }else if (!overlap_correction && ihw_filt) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
401 result_windows[, "p_adj_IHW"] <- adj_pvalues(ihw(pvalue ~ baseMean,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
402 data = result_windows,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
403 alpha = p_value_cutoff,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
404 nfolds = 10))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
405 padj_col <- "p_adj_IHW"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
406 }else if (overlap_correction && !ihw_filt) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
407 padj_col <- "pSlidingWindows.adj"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
408 }else {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
409 result_windows[, "p_adj"] <- p.adjust(result_windows$pvalue, method = "BH")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
410 padj_col <- "p_adj"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
411 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
412
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
413 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
414
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
415 Determine significant windows
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
416
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
417 ```{r filter_sig_windows}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
418 result_windows <- result_windows %>%
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
419 mutate(significant = result_windows[, padj_col] < p_value_cutoff)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
420 sig_windows <- sum(result_windows$significant)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
421 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
422
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
423
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
424 `r sig_windows` windows are significant
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
425
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
426
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
427 ### Combining windows
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
428
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
429 ```{r, reg1, message=FALSE, eval=TRUE, include=FALSE}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
430 if (sig_windows > 0) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
431 result_regions <- extractRegions(windowRes = result_windows, padjCol = padj_col, padjThresh = p_value_cutoff, log2FoldChangeThresh = lfc_cutoff) %>% as_tibble
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
432 }else {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
433 message("Cannot find significant windows in this dataset. Try lowering the p-value and log2FoldChange thresholds!")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
434 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
435 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
436
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
437 ```{r extractRegion, eval=FALSE}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
438 if (sig_windows > 0) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
439 result_regions <- extractRegions(windowRes = result_windows, padjCol = padj_col, padjThresh = p_value_cutoff, log2FoldChangeThresh = lfc_cutoff) %>% as_tibble
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
440 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
441 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
442
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
443
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
444 ### Writing Bed file
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
445
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
446 ```{r writing bed file}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
447 if (sig_windows > 1) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
448 toBED(windowRes = result_windows, regionRes = result_regions, padjThresh = p_value_cutoff, padjCol = padj_col, fileName = output_bed_file)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
449 }else {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
450 message("This analysis does not have enough <=1 significant windows to create BED file for visualization")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
451 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
452 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
453
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
454
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
455 ## Save Session
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
456 ```{r save_data}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
457 # save enriched windows, gzip results file if the file suffix is .gz
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
458 if (grepl("\\.gz$", output_windows_file, ignore.case = TRUE)) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
459 gz_out <- gzfile(output_windows_file, "w")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
460 write.table(result_windows, file = gz_out, sep = "\t", quote = FALSE, row.names = FALSE, col.names = TRUE)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
461 close(gz_out)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
462 }else {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
463 write.table(result_windows, file = output_windows_file, sep = "\t", quote = FALSE, row.names = FALSE, col.names = TRUE)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
464 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
465 # save enriched regions
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
466 if (sig_windows > 0) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
467 if (grepl("\\.gz$", output_regions_file, ignore.case = TRUE)) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
468 gz_out <- gzfile(output_regions_file, "w")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
469 write.table(result_regions, file = gz_out, sep = "\t", quote = FALSE, row.names = FALSE, col.names = TRUE)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
470 close(gz_out)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
471 }else {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
472 write.table(result_regions, file = output_regions_file, sep = "\t", quote = FALSE, row.names = FALSE, col.names = TRUE)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
473 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
474 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
475 # save session
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
476 # Warning! session images can be heavy!
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
477 if (nchar(output_rdata) > 5) {
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
478 save.image(file = output_rdata)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
479 }
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
480 ```
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
481
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
482 ## Session Info
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
483
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
484 ```{r session info}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
485 sessionInfo()
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
486 ```