coverageDepth {ribosomeProfilingQC} | R Documentation |
Calculate the coverage depth for gene level or transcript level. Coverage for RPFs will be the best P site coverage. Coverage for RNAs will be the coverage for 5'end of reads.
coverageDepth( RPFs, RNAs, gtf, level = c("tx", "gene"), bestpsite = 13, readsLen = c(28, 29), anchor = "5end", region = "cds", ext = 5000, ... )
RPFs |
Bam file names of RPFs. |
RNAs |
Bam file names of RNAseq. |
gtf |
GTF file name for annotation or a TxDb object. |
level |
Transcript or gene level. |
bestpsite |
P site postion. |
readsLen |
Reads length to keep. |
anchor |
5end or 3end. Default is 5end. |
region |
Annotation region. It could be "cds", "utr5", "utr3", "exon", "transcripts", "feature with extension". |
ext |
Extesion region for "feature with extension". |
... |
Parameters pass to makeTxDbFromGFF |
A cvgd object with coverage depth.
path <- system.file("extdata", package="ribosomeProfilingQC") RPFs <- dir(path, "RPF.*?\\.[12].bam$", full.names=TRUE) gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz") cvgs <- coverageDepth(RPFs[1], gtf=gtf, level="gene")