getFPKM {ribosomeProfilingQC} | R Documentation

## 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)

[Package ribosomeProfilingQC version 1.6.1 Index]