getFPKM: Get FPKM values for counts

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Get FPKM values for counts

Description

Calculate Fragments Per Kilobase of transcript per Million mapped reads (FPKM) for counts.

Usage

getFPKM(counts, gtf, level = c("gene", "tx"))

Arguments

counts	Output of countReads or normByRUVs
gtf	GTF file name for annotation.
level	Transcript or gene level.

Value

A list with FPKMs

Examples

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)

jianhong/ribosomeProfilingQC documentation built on Nov. 3, 2024, 6:33 p.m.