Mercurial > repos > mingchen0919 > deseq2_rmarkdown

comparison DESeq.Rmd @ 7:a5fdd120b2c7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author mingchen0919
date Mon, 07 Aug 2017 18:11:50 -0400
parents
children
comparison
equal deleted inserted replaced
6:f1e4bfc58975 7:a5fdd120b2c7
1 ---
2 title: 'DESeq2: Perform DESeq analysis'
3 output:
4 html_document:
5 number_sections: true
6 toc: true
7 theme: cosmo
8 highlight: tango
9 ---
10
11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
12 knitr::opts_chunk$set(
13 echo = ECHO
14 )
15
16 library(stringi)
17 library(DESeq2)
18 library(pheatmap)
19 library(PoiClaClu)
20 library(RColorBrewer)
21 ```
22
23 # `DESeqDataSet` object
24
25 ```{r}
26 count_files = strsplit(opt$count_files, ',')[[1]]
27 sample_table = read.table(opt$sample_table, header = TRUE)
28
29 ## copy count files into working directory
30 file_copy = file.copy(count_files, sample_table$fileName, overwrite = TRUE)
31
32 ## DESeqDataSet object
33 dds = DESeqDataSetFromHTSeqCount(sampleTable = sample_table,
34 directory = './',
35 design = DESIGN_FORMULA)
36 dds
37 ```
38
39 # Pre-filtering the dataset.
40
41 We can remove the rows that have 0 or 1 count to reduce object size and increase the calculation speed.
42
43 * Number of rows before pre-filtering
44 ```{r}
45 nrow(dds)
46 ```
47
48 * Number of rows after pre-filtering
49 ```{r}
50 dds = dds[rowSums(counts(dds)) > 1, ]
51 nrow(dds)
52 ```
53
54 # Peek at data {.tabset}
55
56 ## Count Data
57
58 ```{r}
59 datatable(head(counts(dds), 100), style="bootstrap",
60 class="table-condensed", options = list(dom = 'tp', scrollX = TRUE))
61 ```
62
63 ## Sample Table
64
65 ```{r}
66 datatable(sample_table, style="bootstrap",
67 class="table-condensed", options = list(dom = 'tp', scrollX = TRUE))
68 ```
69
70 # Sample distance on variance stabilized data {.tabset}
71
72 ## `rlog` Stabilizing transformation
73
74 ```{r}
75 rld = rlog(dds, blind = FALSE)
76 datatable(head(assay(rld), 100), style="bootstrap",
77 class="table-condensed", options = list(dom = 'tp', scrollX = TRUE))
78 ```
79
80 ## Sample distance
81
82 ```{r}
83 sampleDists <- dist(t(assay(rld)))
84 sampleDists
85 ```
86
87 # Differential expression analysis
88
89 ```{r}
90 dds <- DESeq(dds)
91 ```
92
93 ```{r}
94 rm("opt")
95 save(list=ls(all.names = TRUE), file='DESEQ_WORKSPACE')
96 ```
97
98