Mercurial > repos > proteore > proteore_tissue_specific_expression_data

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