fpkm {ORFik} | R Documentation |
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'.
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. |
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)