readCuffGeneFpkm {spliceSites} | R Documentation |
Opens fpkm_tracking files and collects FPKM values into
ExpressionSet.
The function is intended to work whith genes.fpkm_tracking
files.
In order to get unique gene identifier, the contained values are grouped
and for each gene the maximum FPKM values is selected.
There should only be a few hundred multiple occurring genes and the maximum
value should give a (slight) underestimation of the real value.
readCuffGeneFpkm(cuff, phenoData, summ="max")
cuff |
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phenoData |
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summ |
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ExpressionSet
Wolfgang Kaisers
n<-10 cuff <- system.file("extdata", "cuff_files", paste(1:n, "genes", "fpkm_tracking", sep="."), package="spliceSites") ## Create Pheno - data gr <- system.file("extdata", "cuff_files", "groups.csv", package="spliceSites") groups <- read.table(gr, sep="\t", header=TRUE) meta <- data.frame(labelDescription=c("gender", "age-group", "location"), row.names=c("gen", "agg", "loc")) phenoData <- new("AnnotatedDataFrame", data=groups, varMetadata=meta) ## Read ExpressionSet exset <- readCuffGeneFpkm(cuff, phenoData)