rankOrder {ORFik} | R Documentation |
Creates an ordering of ORFs per transcript, so that ORF with the most upstream start codon is 1, second most upstream start codon is 2, etc. Must input a grl made from ORFik, txNames_2 -> 2.
rankOrder(grl)
grl |
a |
a numeric vector of integers
doi: 10.1074/jbc.R116.733899
Other features:
computeFeaturesCage()
,
computeFeatures()
,
countOverlapsW()
,
disengagementScore()
,
distToCds()
,
distToTSS()
,
entropy()
,
floss()
,
fpkm_calc()
,
fpkm()
,
fractionLength()
,
initiationScore()
,
insideOutsideORF()
,
isInFrame()
,
isOverlapping()
,
kozakSequenceScore()
,
orfScore()
,
ribosomeReleaseScore()
,
ribosomeStallingScore()
,
startRegionCoverage()
,
startRegion()
,
stopRegion()
,
subsetCoverage()
,
translationalEff()
gr_plus <- GRanges(seqnames = c("chr1", "chr1"), ranges = IRanges(c(7, 14), width = 3), strand = c("+", "+")) gr_minus <- GRanges(seqnames = c("chr2", "chr2"), ranges = IRanges(c(4, 1), c(9, 3)), strand = c("-", "-")) grl <- GRangesList(tx1 = gr_plus, tx2 = gr_minus) grl <- ORFik:::makeORFNames(grl) rankOrder(grl)