fractionLength: Fraction Length

In JokingHero/ORFik: Open Reading Frames in Genomics

Fraction Length

Description

Fraction Length is defined as

(widths of grl)/tx_len

so that each group in the grl is divided by the corresponding transcript.

Usage

fractionLength(grl, tx_len = widthPerGroup(tx, TRUE), tx = NULL)

Arguments

grl	a GRangesList object with usually either leaders, cds', 3' utrs or ORFs. ORFs are a special case, see argument tx_len
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)'.
tx	default NULL, a GRangesList object of transcript to get lengths from. Pass in for wrapping to widths inside the function.

Value

a numeric vector of ratios

References

doi: 10.1242/dev.098343

See Also

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

Examples

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, tx = tx)

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