floss: Fragment Length Organization Similarity Score

In JokingHero/ORFik: Open Reading Frames in Genomics

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 read widths) that overlap ORFs and normalize by CDS read width fractions. So if all read length are width 34 in ORFs and CDS, value is 1. If width is 33 in ORFs and 34 in CDS, value is 0. If width is 33 in ORFs and 50/50 (33 and 34) in CDS, values will be 0.5 (for 33).

Usage

floss(grl, RFP, cds, start = 26, end = 34, weight = 1L)

Arguments

grl	a GRangesList object can be either transcripts, 5' utrs, cds', 3' utrs or ORFs as a special case (uORFs, potential new cds' etc). If regions are not spliced you can send a GRanges object.
RFP	ribosomal footprints, given as GAlignments or GRanges object, must be already shifted and resized to the p-site. Requires a $size column with original read lengths.
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 (inclusive)
end	usually 34, the end of the floss interval (inclusive)
weight	a numeric/integer vector or metacolumn name. (default: 1L, no differential weighting). If weight is name of defined meta column in reads object, it gives the number of times a read was found at that position. GRanges("chr1", 1, "+", score = 5), would mean "score" column tells that this alignment region was found 5 times. if 1L it means each read is weighted equal as 1, this is what among others countOverlaps() presumes, if single number (!= 1), it repeats for all ranges, if vector with length > 1, it must be equal size of the reads object.

Details

Pseudo explanation of the function:

SUM[start to stop]((grl[start:end][name]/grl) / (cds[start:end][name]/cds))

Where 'name' is transcript names.
Please read more in the article.

Value

a vector of FLOSS of length same as grl, 0 means no RFP reads in range, 1 is perfect match.

References

doi: 10.1016/j.celrep.2014.07.045

See Also

Other features: computeFeatures(), computeFeaturesCage(), countOverlapsW(), disengagementScore(), distToCds(), distToTSS(), entropy(), fpkm(), fpkm_calc(), fractionLength(), initiationScore(), insideOutsideORF(), isInFrame(), isOverlapping(), kozakSequenceScore(), orfScore(), rankOrder(), ribosomeReleaseScore(), ribosomeStallingScore(), startRegion(), startRegionCoverage(), stopRegion(), subsetCoverage(), translationalEff()

Examples

ORF1 <- GRanges(seqnames = "1",
               ranges = IRanges(start = c(1, 12, 22),
               end = c(10, 20, 32)),
               strand = "+")
grl <- GRangesList(tx1_1 = ORF1)
# RFP is 1 width position based GRanges
RFP <- GRanges("1", IRanges(c(1, 25, 35, 38), width = 1), "+")
RFP$size <- c(28, 28, 28, 29) # original width in size 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)

# With repeated alignments in score column
ORF2 <- GRanges(seqnames = "1",
               ranges = IRanges(start = c(12, 22, 36),
               end = c(20, 32, 38)),
               strand = "+")
grl <- GRangesList(tx1_1 = ORF1, tx1_2 = ORF2)
score(RFP) <- c(5, 10, 5, 10)
floss(grl, RFP, cds, weight = "score")

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.