fpkm {ORFik}R Documentation

Create normalizations of overlapping read counts.

Description

FPKM is short for "Fragments Per Kilobase of transcript per Million fragments". When calculating RiboSeq data FPKM over ORFs, use ORFs as 'grl'. When calculating RNASeq data FPKM, use full transcripts as 'grl'.

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).

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.

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 1.4.0 Index]