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comparison ImportDataFromMatrix.R @ 6:3ce32282f6a4 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 228bd64b01f184d5d8ebc9f65fe0add2d45ed4fe
author sblanck
date Tue, 26 Jun 2018 08:54:45 -0400
parents 1024245abc70
children
comparison
equal deleted inserted replaced
5:ca46ad51fe5a 6:3ce32282f6a4
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 head(data) 60 eset=ExpressionSet(assayData=data,annotation=annotation)
70 conditions
71
72 eset=ExpressionSet(assayData=data,phenoData=phenodata,annotation=annotation)
73 61
74 if (normalization == "quantile") { 62 if (normalization == "quantile") {
75 eset <- normalize.ExpressionSet.quantiles(eset, transfn="log2") 63 eset <- normalize.ExpressionSet.quantiles(eset, transfn="log")
76 } else if (normalization == "log2") { 64 } else if (normalization == "log2") {
77 exprs(eset) = log2(exprs(eset)) 65 exprs(eset) = log2(exprs(eset))
78 } 66 }
79 67
80 boxplotnorm="boxplotnorm.png" 68 boxplotnorm="boxplotnorm.png"