translationalEff {ORFik}R Documentation

Translational efficiency

Description

Uses RnaSeq and RiboSeq to get translational efficiency of every element in 'grl'. Translational efficiency is defined as:

(density of RPF within ORF) / (RNA expression of ORFs transcript)

Usage

translationalEff(grl, RNA, RFP, tx, with.fpkm = FALSE, pseudoCount = 0)

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).

RNA

RnaSeq reads as GAlignment, GRanges or GRangesList object

RFP

RiboSeq reads as GAlignment, GRanges or GRangesList object

tx

a GRangesList of the transcripts. If you used cage data, then the tss for the the leaders have changed, therefor the tx lengths have changed. To account for that call: ' translationalEff(grl, RNA, RFP, tx = extendLeaders(tx, cageFiveUTRs)) ' where cageFiveUTRs are the reannotated by CageSeq data leaders.

with.fpkm

logical F, if true return the fpkm values together with translational efficiency

pseudoCount

an integer, 0, set it to 1 if you want to avoid NA and inf values. It also helps against bias from low depth libraries.

Value

a numeric vector of fpkm ratios, if with.fpkm is TRUE, return a data.table with te and fpkm values

References

doi: 10.1126/science.1168978

See Also

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

Examples

ORF <- GRanges(seqnames = "1",
               ranges = IRanges(start = c(1, 10, 20), end = c(5, 15, 25)),
               strand = "+")
grl <- GRangesList(tx1_1 = ORF)
RFP <- GRanges("1", IRanges(25, 25), "+")
RNA <- GRanges("1", IRanges(1, 50), "+")
tx <-  GRangesList(tx1 = GRanges("1", IRanges(1, 50), "+"))
# grl must have same names as cds + _1 etc, so that they can be matched.
te <- translationalEff(grl, RNA, RFP, tx, with.fpkm = TRUE, pseudoCount = 1)
te$fpkmRFP
te$te


[Package ORFik version 1.4.0 Index]