Mercurial > repos > proteore > proteore_tissue_specific_expression_data

comparison RetrieveFromHPA.R @ 0:8ff819779f7e draft

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planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty
author proteore
date Wed, 14 Mar 2018 11:36:19 -0400
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-1:000000000000 0:8ff819779f7e
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3 select.HPAimmunohisto<-function(hpa_ref, tissue, level, reliability) {
4 load(hpa_ref)
5 if (tissue == "tissue") {
6 tissue <- unique(HPA.normal$Tissue)
7 }
8 if (level == "level") {
9 level <- unique(HPA.normal$Level)
10 }
11 if (reliability == "reliability") {
12 reliability <- unique(HPA.normal$Reliability)
13 }
14 res.imm <- subset(HPA.normal, Tissue%in%tissue & Level%in%level & Reliability%in%reliability)
15 return(res.imm)
16 }
17
18
19
20 select.HPARNAseq<-function(hpa_ref, sample) {
21 load(hpa_ref)
22 res.rna <- subset(HPA.rnaTissue, Sample%in%sample, select = -c(Unit))
23 colnames(res.rna)[which(colnames(res.rna) == 'Value')] <- 'Value (TPM unit)'
24 return(res.rna)
25 }
26
27 main <- function() {
28 args <- commandArgs(TRUE)
29 if(length(args)<1) {
30 args <- c("--help")
31 }
32
33 # Help section
34 if("--help" %in% args) {
35 cat("Selection and Annotation HPA
36 Arguments:
37 --data_source: immuno/rnaseq
38 --hpe_ref: path to reference file (HPA.normal.RData/HPA.rnaTissue.RData)
39 if immuno:
40 --tissue: list of tissues
41 --level: Not detected, Low, Medium, High
42 --reliability: Supported, Approved, Enhanced, Uncertain
43 if rnaseq:
44 --sample: Sample tissues
45 --output: output filename \n")
46 q(save="no")
47 }
48
49 # Parse arguments
50 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
51 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
52 args <- as.list(as.character(argsDF$V2))
53 names(args) <- argsDF$V1
54
55 # Extract options
56 data_source = args$data_source
57 hpa_ref = args$hpa_ref
58 if (data_source == "immuno") {
59 tissue = strsplit(args$tissue, ",")[[1]]
60 level = strsplit(args$level, ",")[[1]]
61 reliability = strsplit(args$reliability, ",")[[1]]
62 # Calculation
63 res = select.HPAimmunohisto(hpa_ref, tissue, level, reliability)
64 }
65 else if (data_source == "rnaseq") {
66 sample = strsplit(args$sample, ",")[[1]]
67 # Calculation
68 res = select.HPARNAseq(hpa_ref, sample)
69 }
70
71 # Write output
72 output = args$output
73 write.table(res, output, sep = "\t", quote = FALSE, row.names = FALSE)
74 }
75
76 main()