fpkm {ORFik} | R Documentation |
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.
fpkm(grl, reads, pseudoCount = 0)
grl |
a |
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. |
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]
a numeric vector with the fpkm values
doi: 10.1038/nbt.1621
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()
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)