fractionLength {ORFik} | R Documentation |
Fraction Length is defined as
(widths of grl)/tx_len
so that each group in the grl is divided by the corresponding transcript.
fractionLength(grl, tx_len)
grl |
a |
tx_len |
the transcript lengths of the transcripts, a named (tx names) vector of integers. If you have the transcripts as GRangesList, call 'ORFik:::widthPerGroup(tx, TRUE)'. If you used CageSeq to reannotate leaders, then the tss for the the leaders have changed, therefore the tx lengths have changed. To account for that call: 'tx_len <- widthPerGroup(extendLeaders(tx, cageFiveUTRs))' and calculate fraction length using 'fractionLength(grl, tx_len)'. |
a numeric vector of ratios
doi: 10.1242/dev.098343
Other features:
computeFeaturesCage()
,
computeFeatures()
,
countOverlapsW()
,
disengagementScore()
,
distToCds()
,
distToTSS()
,
entropy()
,
floss()
,
fpkm_calc()
,
fpkm()
,
initiationScore()
,
insideOutsideORF()
,
isInFrame()
,
isOverlapping()
,
kozakSequenceScore()
,
orfScore()
,
rankOrder()
,
ribosomeReleaseScore()
,
ribosomeStallingScore()
,
startRegionCoverage()
,
startRegion()
,
stopRegion()
,
subsetCoverage()
,
translationalEff()
ORF <- GRanges(seqnames = "1", ranges = IRanges(start = c(1, 10, 20), end = c(5, 15, 25)), strand = "+") grl <- GRangesList(tx1_1 = ORF) # grl must have same names as cds + _1 etc, so that they can be matched. tx <- GRangesList(tx1 = GRanges("1", IRanges(1, 50), "+")) fractionLength(grl, ORFik:::widthPerGroup(tx, keep.names = TRUE))