ribosomeReleaseScore {ribosomeProfilingQC} | R Documentation |
RRS is calculated as the ratio of translational efficiency in the CDS with RPFs in the 3'UTR.
ribosomeReleaseScore( cdsTE, utr3TE, CDSsampleOrder, UTR3sampleOrder, pseudocount = 0, log2 = FALSE )
cdsTE, utr3TE |
Translational efficiency of CDS and UTR3 region. Output of translationalEfficiency |
CDSsampleOrder, UTR3sampleOrder |
Sample order of cdsTE and utr3TE. The parameters are used to make sure that the order of CDS and UTR3 in TE is corresponding samples. |
pseudocount |
The number will be add to sum of reads count to avoid X/0. |
log2 |
Do log2 transform or not. |
A vector of RRS.
## Not run: path <- system.file("extdata", package="ribosomeProfilingQC") RPFs <- dir(path, "RPF.*?\\.[12].bam$", full.names=TRUE) RNAs <- dir(path, "mRNA.*?\\.[12].bam$", full.names=TRUE) gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz") cvgs <- coverageDepth(RPFs, RNAs, gtf) cvgs.utr3 <- coverageDepth(RPFs, RNAs, gtf, region="utr3") TE90 <- translationalEfficiency(cvgs, window = 90) TE90.utr3 <- translationalEfficiency(cvgs.utr3, window = 90) rrs <- ribosomeReleaseScore(TE90, TE90.utr3) ## End(Not run)