floss {ORFik}R Documentation

Fragment Length Organization Similarity Score

Description

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.

Usage

floss(grl, RFP, cds, start = 26, end = 34)

Arguments

grl

a GRangesList object with ORFs

RFP

ribosomal footprints, given as Galignment or GRanges object, must be already shifted and resized to the p-site

cds

a GRangesList of coding sequences, cds has to have names as grl so that they can be matched

start

usually 26, the start of the floss interval

end

usually 34, the end of the floss interval

Details

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.

Value

a vector of FLOSS of length same as grl

References

doi: 10.1016/j.celrep.2014.07.045

See Also

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

Examples

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)


[Package ORFik version 1.4.0 Index]