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comparison ImportDataFromMatrix.R @ 38:c08b824e40cc draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 86c0c3bb957558f14e9400171640bf5a5c6605c9
author sblanck
date Mon, 25 Jun 2018 05:25:40 -0400
parents 25b828010ca9
children
comparison
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37:25b828010ca9 38:c08b824e40cc
8 library("optparse") 8 library("optparse")
9 9
10 ##### Read options 10 ##### Read options
11 option_list=list( 11 option_list=list(
12 make_option("--input",type="character",default="NULL",help="rdata object containing eset object"), 12 make_option("--input",type="character",default="NULL",help="rdata object containing eset object"),
13 make_option("--conditions",type="character",default=NULL,help="Text file summarizing conditions of the experiment (required)"),
14 make_option("--normalization",type="character",default=NULL,help="log2 transformation"), 13 make_option("--normalization",type="character",default=NULL,help="log2 transformation"),
15 make_option("--annotations",type="character",default="NULL",help="rdata object containing eset object"), 14 make_option("--annotations",type="character",default="NULL",help="rdata object containing eset object"),
16 make_option("--rdataoutput",type="character",default="NULL",help="output rdata object containing eset object"), 15 make_option("--rdataoutput",type="character",default="NULL",help="output rdata object containing eset object"),
17 make_option("--htmloutput",type="character",default=NULL,help="Output html report"), 16 make_option("--htmloutput",type="character",default=NULL,help="Output html report"),
18 make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"), 17 make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"),
28 if(is.null(opt$input)){ 27 if(is.null(opt$input)){
29 print_help(opt_parser) 28 print_help(opt_parser)
30 stop("input required.", call.=FALSE) 29 stop("input required.", call.=FALSE)
31 } 30 }
32 31
33 if(is.null(opt$conditions)){
34 print_help(opt_parser)
35 stop("conditions input required.", call.=FALSE)
36 }
37 32
38 33
39 #loading libraries 34 #loading libraries
40 suppressPackageStartupMessages(require(GEOquery))
41
42 suppressPackageStartupMessages(require(Biobase)) 35 suppressPackageStartupMessages(require(Biobase))
43 suppressPackageStartupMessages(require(GEOquery))
44 suppressPackageStartupMessages(require(GEOmetadb))
45 suppressPackageStartupMessages(require(limma)) 36 suppressPackageStartupMessages(require(limma))
46 suppressPackageStartupMessages(require(jsonlite)) 37 suppressPackageStartupMessages(require(jsonlite))
47 suppressPackageStartupMessages(require(affy)) 38 suppressPackageStartupMessages(require(affy))
48 suppressPackageStartupMessages(require(dplyr)) 39 suppressPackageStartupMessages(require(dplyr))
49 suppressPackageStartupMessages(require(affyPLM)) 40 suppressPackageStartupMessages(require(affyPLM))
58 result.template=opt$htmltemplate 49 result.template=opt$htmltemplate
59 50
60 dir.create(result.path, showWarnings = TRUE, recursive = FALSE) 51 dir.create(result.path, showWarnings = TRUE, recursive = FALSE)
61 52
62 data=as.matrix(read.table(file = dataFile,row.names=1,header=TRUE)) 53 data=as.matrix(read.table(file = dataFile,row.names=1,header=TRUE))
63 conditions=read.table(file=conditionsFile,sep = "\t",row.names=1) 54 #conditions=read.table(file=conditionsFile,sep = "\t",row.names=1)
64 htmlfile=readChar(result.template, file.info(result.template)$size) 55 htmlfile=readChar(result.template, file.info(result.template)$size)
65 56
66 colnames(conditions)=c("source_name_ch1","description") 57 #colnames(conditions)=c("source_name_ch1","description")
67 phenodata<-new("AnnotatedDataFrame",data=conditions) 58 #phenodata<-new("AnnotatedDataFrame",data=conditions)
68 59
69 eset=ExpressionSet(assayData=data,phenoData=phenodata,annotation=annotation) 60 eset=ExpressionSet(assayData=data,annotation=annotation)
70 61
71 if (normalization == "quantile") { 62 if (normalization == "quantile") {
72 eset <- normalize.ExpressionSet.quantiles(eset, transfn="log") 63 eset <- normalize.ExpressionSet.quantiles(eset, transfn="log")
73 } else if (normalization == "log2") { 64 } else if (normalization == "log2") {
74 exprs(eset) = log2(exprs(eset)) 65 exprs(eset) = log2(exprs(eset))