getPsiteCoordinates {ribosomeProfilingQC} | R Documentation |
Extract P site coordinates from a bam file to a GRanges object.
getPsiteCoordinates(bamfile, bestpsite, anchor = "5end")
bamfile |
A BamFile object. |
bestpsite |
P site postion. See estimatePsite |
anchor |
5end or 3end. Default is 5end. |
A GRanges object with qwidth metadata which indicates the width of reads.
library(Rsamtools) bamfilename <- system.file("extdata", "RPF.WT.1.bam", package="ribosomeProfilingQC") yieldSize <- 10000000 bamfile <- BamFile(bamfilename, yieldSize = yieldSize) pc <- getPsiteCoordinates(bamfile, bestpsite=13)