readsDistribution {ribosomeProfilingQC} | R Documentation |
Plot the percentage of reads in CDS, 5'UTR, 3'UTR, introns, and other elements.
readsDistribution( reads, txdb, upstreamRegion = 3000, downstreamRegion = 3000, plot = TRUE, ... )
reads |
Output of getPsiteCoordinates |
txdb |
A TxDb object |
upstreamRegion, downstreamRegion |
The range for promoter region and downstream region. |
plot |
Plot the distribution or not |
... |
Not use. |
The reads with distribution assignment
library(Rsamtools) bamfilename <- system.file("extdata", "RPF.WT.1.bam", package="ribosomeProfilingQC") yieldSize <- 10000000 bamfile <- BamFile(bamfilename, yieldSize = yieldSize) pc <- getPsiteCoordinates(bamfile, bestpsite=11) pc.sub <- pc[pc$qwidth %in% c(29, 30)] library(GenomicFeatures) library(BSgenome.Drerio.UCSC.danRer10) txdb <- makeTxDbFromGFF(system.file("extdata", "Danio_rerio.GRCz10.91.chr1.gtf.gz", package="ribosomeProfilingQC"), organism = "Danio rerio", chrominfo = seqinfo(Drerio)["chr1"], taxonomyId = 7955) pc.sub <- readsDistribution(pc.sub, txdb, las=2)