getFPKM {ribosomeProfilingQC} | R Documentation |
Calculate Fragments Per Kilobase of transcript per Million mapped reads (FPKM) for counts.
getFPKM(counts, gtf, level = c("gene", "tx"))
counts |
Output of countReads or normByRUVs |
gtf |
GTF file name for annotation. |
level |
Transcript or gene level. |
A list with FPKMs
path <- system.file("extdata", package="ribosomeProfilingQC") #RPFs <- dir(path, "RPF.*?.[12].bam$", full.names=TRUE) #RNAs <- dir(path, "mRNA.*?.[12].bam$", full.names=TRUE) #gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz") #cnts <- countReads(RPFs, RNAs, gtf, level="gene") cnts <- readRDS(file.path(path, "cnts.rds")) fpkm <- getFPKM(cnts)