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comparison MetaMA.R @ 20:a4015af2ae12 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d
author sblanck
date Mon, 15 Jan 2018 04:50:08 -0500
parents 56267e3293b2
children f953fdee364c
comparison
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19:c08d47a36c1f 20:a4015af2ae12
7 7
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="list of rdata objects containing eset objects"), 12 make_option("--input",type="character",default="NULL",help="List of rdata objects containing eset objects"),
13 make_option("--species",type="character",default="NULL",help="Species for annotations"),
13 make_option("--htmloutput",type="character",default=NULL,help="Output html report"), 14 make_option("--htmloutput",type="character",default=NULL,help="Output html report"),
14 make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"), 15 make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"),
15 make_option("--htmltemplate",type="character",default=NULL,help="html template)") 16 make_option("--htmltemplate",type="character",default=NULL,help="html template)")
16 ); 17 );
17 18
18 opt_parser = OptionParser(option_list=option_list); 19 opt_parser = OptionParser(option_list=option_list);
19 opt = parse_args(opt_parser); 20 opt = parse_args(opt_parser);
20 21
21 if(is.null(opt$input)){ 22 if(is.null(opt$input)){
23 print_help(opt_parser)
24 stop("input required.", call.=FALSE)
25 }
26 if(is.null(opt$species)){
22 print_help(opt_parser) 27 print_help(opt_parser)
23 stop("input required.", call.=FALSE) 28 stop("input required.", call.=FALSE)
24 } 29 }
25 30
26 #loading libraries 31 #loading libraries
30 suppressPackageStartupMessages(require(annaffy)) 35 suppressPackageStartupMessages(require(annaffy))
31 suppressPackageStartupMessages(require(VennDiagram)) 36 suppressPackageStartupMessages(require(VennDiagram))
32 suppressPackageStartupMessages(require(GEOquery)) 37 suppressPackageStartupMessages(require(GEOquery))
33 38
34 listInput <- trimws( unlist( strsplit(trimws(opt$input), ",") ) ) 39 listInput <- trimws( unlist( strsplit(trimws(opt$input), ",") ) )
40 species=opt$species
35 41
36 rdataList=list() 42 rdataList=list()
37 condition1List=list() 43 condition1List=list()
38 condition2List=list() 44 condition2List=list()
39 for (input in listInput) 45 for (input in listInput)
59 jpeg(file) 65 jpeg(file)
60 grid.draw(venn.plot) 66 grid.draw(venn.plot)
61 dev.off() 67 dev.off()
62 } 68 }
63 69
64 library("org.Hs.eg.db") 70 if(!species %in% installed.packages()[,"Package"]) {
71 source("https://bioconductor.org/biocLite.R")
72 biocLite(species)
73 }
74
75 #library("org.Hs.eg.db")
65 x <- org.Hs.egUNIGENE 76 x <- org.Hs.egUNIGENE
66 mapped_genes <- mappedkeys(x) 77 mapped_genes <- mappedkeys(x)
67 link <- as.list(x[mapped_genes]) 78 link <- as.list(x[mapped_genes])
68 79
69 probe2unigene<-function(expset){ 80 probe2unigene<-function(expset){