strandPlot {ribosomeProfilingQC} | R Documentation |
Plot the distribution of reads in sense and antisense strand to check the mapping is correct.
strandPlot(reads, CDS, col = c("#009E73", "#D55E00"), ...)
reads |
Output of getPsiteCoordinates |
CDS |
Output of prepareCDS |
col |
Coloar for sense and antisense strand. |
... |
Parameter passed to barplot |
A ggplot object.
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) CDS <- prepareCDS(txdb) strandPlot(pc.sub, CDS)