sam.stats: Get summary statistics for bam files

In dvera/travis: R Utilities for Bed and BEdgRaphs

Description

Calculates the number of duplicate, unique-aligning, multi-aligning, unaligned, and total reads for a set of position-sorted bam files.

Usage

sam.stats(bamFiles, genomefile, probes = NULL, expandprobes = 200,
  plot = TRUE, uniquescore = 10, cores = 11)

Arguments

bamFiles	a character vector of paths to position-sorted bam files
genomefile	a string of the path to the genome file, a tab-delimited file with chromosome names in column 1 and chromosome sizes in column 2
probes	a string of the path to a bed file containing the locations of specific regions of interest to additionally calculate the overlap of reads to these regions
expandprobes	a positive integer that is used to expand the region around intervals in 'probes' in which to calculate overlap of reads
plot	boolean indicating if a summary plot is drawn for calculated statistics
uniquescore	a positive integer used as the threshold for calling an alignment unique
cores	a positive integer specifying the number of bam files to process simultaneously

dvera/travis documentation built on June 5, 2019, 5:12 a.m.