get_pileup: Get the pileup-statistics from a bam file using Rsamtools

In phac-nml/pavian: Visualize and analyze metagenomics classification results

Description

Returns per-base pileup statistics, or a moving average. TODO: Non-overlapping mean is probably the better idea, here, as only one value per bin is reported

Usage

get_pileup(bam_file, min_mapq = 0, top_n = NULL, ...)

Arguments

bam_file	character(1) or BamFile; BAM file path.
min_mapq	Minimum mapping quality.
top_n	If not NULL, return at most the pileups of that many sequences. integer(1).
...	Additional arguments for Rsamtools::pileup

Value

data.frame with sequence names, positions, strand and count information

phac-nml/pavian documentation built on Aug. 20, 2019, 5:54 a.m.