Mercurial > repos > yhoogstrate > edger_with_design_matrix

comparison edgeR_DGE.xml @ 12:c672e76503b2 draft

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author yhoogstrate
date Thu, 09 Jan 2014 06:55:28 -0500
parents b8b3d63b60ab
children 6e475c849a38
comparison
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11:b8b3d63b60ab 12:c672e76503b2
66 66
67 library(edgeR) 67 library(edgeR)
68 raw_data <- read.delim(designmatrix,header=T,stringsAsFactors=T) 68 raw_data <- read.delim(designmatrix,header=T,stringsAsFactors=T)
69 69
70 ## Obtain read-counts 70 ## Obtain read-counts
71 read_counts = read.delim(as.character(raw_data[1,1]),header=F,stringsAsFactors=F,row.names=1) 71
72 header = read.delim(as.character(raw_data[1,1]),header=F,stringsAsFactors=F,row.names=1,nrows=1)
73 has_header = (class(header[1,1]) == "character")
74
75 read_counts = read.delim(as.character(raw_data[1,1]),header=has_header,stringsAsFactors=F,row.names=1)
76
72 for(i in 2:length(raw_data[,1])) { 77 for(i in 2:length(raw_data[,1])) {
73 print("parsing counts from:") 78 print("parsing counts from:")
74 print(raw_data[i,1]) 79 print(raw_data[i,1])
75 80
76 header = read.delim(as.character(raw_data[i,1]),header=F,stringsAsFactors=F,row.names=1,nrows=1) 81 header = read.delim(as.character(raw_data[i,1]),header=F,stringsAsFactors=F,row.names=1,nrows=1)