getFragmentWidths {alpine} | R Documentation |
From a BAM file and a particular transcript (recommened to be the single isoform of a gene), this function returns estimates of the fragment widths, by mapping the fragment alignments to the transcript coordinates.
getFragmentWidths(bam.file, tx)
bam.file |
a character string pointing to a BAM file |
tx |
a GRanges object of the exons of a single isoform gene |
a numeric vector of estimated fragment widths
# these next lines just write out a BAM file from R # typically you would already have a BAM file library(alpineData) library(GenomicAlignments) library(rtracklayer) gap <- ERR188088() dir <- system.file(package="alpineData", "extdata") bam.file <- c("ERR188088" = file.path(dir,"ERR188088.bam")) export(gap, con=bam.file) data(preprocessedData) w <- getFragmentWidths(bam.file, ebt.fit[[2]]) quantile(w, c(.025, .975))