countReads {ribosomeProfilingQC} | R Documentation |
Calculate the reads counts for gene level or transcript level.
countReads( RPFs, RNAs, gtf, level = c("tx", "gene"), bestpsite = 13, readsLen = c(28, 29), anchor = "5end", ... )
RPFs |
Bam file names of RPFs. |
RNAs |
Bam file names of RNAseq. |
gtf |
GTF file name for annotation. |
level |
Transcript or gene level. |
bestpsite |
numeric(1). P site postion. |
readsLen |
numeric(1). reads length to keep. |
anchor |
5end or 3end. Default is 5end. |
... |
Parameters pass to featureCounts |
A list with reads counts.
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") cnts <- countReads(RPFs[1], gtf=gtf, level="gene", readsLen=29)