Description Usage Arguments Value Author(s) Examples
Get the total number of genes expressed per gtf file (generated via Cufflinks).
1 | GetNumGenesExpressed(gtfDFs, covThreshold = 1)
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gtfDFs |
data table structure containing Cufflinks results. |
covThreshold |
only genes will be count that have "cov" values above this threshold. Default value is 1.0. |
An integer for the total number of genes expressed per gtf file (generated via Cufflinks).
Nathaniel J. Madrid, Jason Byars
1 2 3 4 5 6 7 | gtffiles <- c("transcripts_sorted.gtf")
FileCons <- mclapply(gtffiles, function(FileName) file(FileName), mc.cores=8)
gtfs <- mclapply(FileCons, function(fc) import.gff(fc, format="gtf"), mc.cores=8)
for(i in length(FileCons)) { close(FileCons[[i]]) }
gtfDFs <- mclapply(gtfs, function(gtf) as.data.frame(gtf[gtf$type=="transcript"]), mc.cores=8)
names(gtfDFs) <- basename(gtffiles)
NumGenesPerFile <- GetNumGenesExpressed(gtfDFs, 1.0)
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