fractionLength {ORFik}

R Documentation

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)

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)'.

Value

a numeric vector of ratios

References

doi: 10.1242/dev.098343

See Also

Other features: computeFeaturesCage(), computeFeatures(), countOverlapsW(), disengagementScore(), distToCds(), distToTSS(), entropy(), floss(), fpkm_calc(), fpkm(), initiationScore(), insideOutsideORF(), isInFrame(), isOverlapping(), kozakSequenceScore(), orfScore(), rankOrder(), ribosomeReleaseScore(), ribosomeStallingScore(), startRegionCoverage(), startRegion(), 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, ORFik:::widthPerGroup(tx, keep.names = TRUE))

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