translationalEfficiency {ribosomeProfilingQC} | R Documentation |
Calculate Translational Efficiency (TE). TE is defined as the ratios of the absolute level of ribosome occupancy devided by RNA levels for transcripts.
translationalEfficiency( x, window, RPFsampleOrder, mRNAsampleOrder, pseudocount = 1, log2 = FALSE, normByLibSize = FALSE )
x |
Output of getFPKM or normByRUVs. if window is set, it must be output of coverageDepth. |
window |
numeric(1). window size for maximal counts. |
RPFsampleOrder, mRNAsampleOrder |
Sample order of RPFs and mRNAs. The parameters are used to make sure that the order of RPFs and mRNAs in cvgs is corresponding samples. |
pseudocount |
The number will be add to sum of reads count to avoid X/0. |
log2 |
Do log2 transform or not. |
normByLibSize |
Normlization by library size or not. If window size is provied and normByLibSize is set to TRUE, the coverage will be normalized by library size. |
A list with RPFs, mRNA levels and TE as a matrix with translational efficiency
## 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") cnts <- countReads(RPFs, RNAs, gtf, level="gene") fpkm <- getFPKM(cnts) te <- translationalEfficiency(fpkm) ## End(Not run)