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18
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1 # loadCountData
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2 # loads counts, one file per lane
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3 # file names from target file
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4
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5 # input : target
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6 # output : raw count table
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7
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8 # created Feb 6th, 2012
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9 # modified May 2nd, 2012 (colnames -> target$label)
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10 # Marie-Agnes Dillies
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11
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12
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13 loadCountData <- function(target, header){
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14
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15 require(DESeq)
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16 fileNames <- target$files
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17
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18 if(header!=0){
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19 #rawCounts <- read.table(as.character(paste(rawDir,target$files[1],sep="/")), sep="\t", header=TRUE)
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20 rawCounts <- read.table(as.character(target$files[1],sep="/"), sep="\t", header=TRUE)
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21 } else if(header==0){
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22 rawCounts <- read.table(as.character(target$files[1],sep="/"), sep="\t")}
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23
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24 colnames(rawCounts) <- c("Id", as.character(target$label[1]))
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25
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26 for (i in 2:length(fileNames)){
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27 if(header!=0){
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28 tmp <- read.table(as.character(target$files[i],sep="/"), sep="\t", header=TRUE)
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29 } else if(header==0){
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30 tmp <- read.table(as.character(target$files[i],sep="/"), sep="\t")}
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31 colnames(tmp) <- c("Id", as.character(target$label[i]))
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32 rawCounts <- merge(rawCounts, tmp, by="Id", all=T)
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33 }
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34 rawCounts[is.na(rawCounts)] <- 0
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35 return(rawCounts)
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36 }
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