fpkm {ORFik} | R Documentation

## Create normalizations of overlapping read counts.

### Description

FPKM is short for "Fragments Per Kilobase of transcript per Million fragments in library". When calculating RiboSeq data FPKM over ORFs, use ORFs as 'grl'. When calculating RNASeq data FPKM, use full transcripts as 'grl'. It is equal to RPKM given that you do not have paired end reads.

### Usage

    fpkm(grl, reads, pseudoCount = 0)

### Arguments

`grl` | a `GRangesList` object can be either transcripts, 5' utrs, cds', 3' utrs or ORFs as a special case (uORFs, potential new cds' etc). If regions are not spliced you can send a `GRanges` object.
`reads` | a GAlignment, GRanges or GRangesList object, usually of RiboSeq, RnaSeq, CageSeq, etc.
`pseudoCount` | an integer, by default is 0, set it to 1 if you want to avoid NA and inf values.

### Details

Note also that you must consider if you will use the whole read library or just the reads overlapping 'grl'. To only overlap do: reads <- reads[countOverlaps(reads, grl) > 0]

### Value

a numeric vector with the fpkm values

### References

doi: 10.1038/nbt.1621

### See Also

Other features: `computeFeaturesCage()`, `computeFeatures()`, `disengagementScore()`, `distToCds()`, `distToTSS()`, `entropy()`, `floss()`, `fpkm_calc()`, `fractionLength()`, `initiationScore()`, `insideOutsideORF()`, `isInFrame()`, `isOverlapping()`, `kozakSequenceScore()`, `orfScore()`, `rankOrder()`, `ribosomeReleaseScore()`, `ribosomeStallingScore()`, `startRegionCoverage()`, `startRegion()`, `subsetCoverage()`, `translationalEff()`

### Examples

    ORF <- GRanges(seqnames = "1",
                   ranges = IRanges(start = c(1, 10, 20),
                   end = c(5, 15, 25)),
                   strand = "+")
    grl <- GRangesList(tx1_1 = ORF)
    RFP <- GRanges("1", IRanges(25, 25),"+")
    fpkm(grl, RFP)

[Package ORFik version 1.6.9 Index]