floss {ORFik} | R Documentation |
This feature is usually calcualted only for RiboSeq reads. For reads of width between 'start' and 'end', sum the fraction of RiboSeq reads (per widths) that overlap ORFs and normalize by CDS.
floss(grl, RFP, cds, start = 26, end = 34)
grl |
a |
RFP |
ribosomal footprints, given as Galignment or GRanges object, must be already shifted and resized to the p-site |
cds |
a |
start |
usually 26, the start of the floss interval |
end |
usually 34, the end of the floss interval |
Pseudo explanation of the function:
SUM[start to stop]((grl[start:end][name]/grl) / (cds[start:end][name]/cds))
Please read more in the article.
a vector of FLOSS of length same as grl
doi: 10.1016/j.celrep.2014.07.045
Other features: computeFeaturesCage
,
computeFeatures
,
disengagementScore
,
distToCds
, distToTSS
,
entropy
, fpkm_calc
,
fpkm
, fractionLength
,
initiationScore
,
insideOutsideORF
, isInFrame
,
isOverlapping
,
kozakSequenceScore
, orfScore
,
rankOrder
,
ribosomeReleaseScore
,
ribosomeStallingScore
,
startRegionCoverage
,
startRegion
, subsetCoverage
,
translationalEff
ORF <- GRanges(seqnames = "1", ranges = IRanges(start = c(1, 12, 22), end = c(10, 20, 32)), strand = "+") grl <- GRangesList(tx1_1 = ORF) # RFP is 1 width position based GRanges RFP <- GRanges("1", IRanges(c(1, 25, 35, 38), width = 1), "+") score(RFP) <- c(28, 28, 28, 29) # original width in score col cds <- GRangesList(tx1 = GRanges("1", IRanges(35, 44), "+")) # grl must have same names as cds + _1 etc, so that they can be matched. floss(grl, RFP, cds) # or change ribosome start/stop, more strict floss(grl, RFP, cds, 28, 28)