translationalEff: Translational efficiency

In Roleren/ORFik: Open Reading Frames in Genomics

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,
  librarySize = "full",
  weight.RFP = 1L,
  weight.RNA = 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.
RNA	RnaSeq reads as GAlignments, GRanges or GRangesList object
RFP	RiboSeq reads as GAlignments, 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, default: FALSE, if true return the fpkm values together with translational efficiency as a data.table
pseudoCount	an integer, by default is 0, set it to 1 if you want to avoid NA and inf values.
librarySize	either numeric value or character vector. Default ("full"), number of alignments in library (reads). If you just have a subset, you can give the value by librarySize = length(wholeLib) or sum(wholeLib$score), if you want lib size to be only number of reads overlapping grl, do: librarySize = "overlapping" sum(countOverlaps(reads, grl) > 0), if reads[1] has 3 hits in grl, and reads[2] has 2 hits, librarySize will be 2, not 5. You can also get the inverse overlap, if you want lib size to be total number of overlaps, do: librarySize = "DESeq" This is standard fpkm way of DESeq2::fpkm(robust = FALSE) sum(countOverlaps(grl, reads)) if grl[1] has 3 reads and grl[2] has 2 reads, librarySize is 5, not 2.
weight.RFP	a vector (default: 1L). Can also be character name of column in RFP. As in translationalEff(weight = "score") for: GRanges("chr1", 1, "+", score = 5), would mean score column tells that this alignment region was found 5 times.
weight.RNA	Same as weightRFP but for RNA weights. (default: 1L)

Value

a numeric vector of fpkm ratios, if with.fpkm is TRUE, return a data.table with te and fpkm values (total 3 columns then)

References

doi: 10.1126/science.1168978

See Also

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

Roleren/ORFik documentation built on Oct. 19, 2024, 7:37 a.m.