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

[Package ORFik version 1.12.13 Index]