getMT: grab the mitochondrial reads from a BAM & estimate their...

In MTseeker: Bioconductor Tools for Human Mitochondrial Variant Analysis

Description

This purely a convenience function, and an incredibly convenient one at that.

Usage

getMT(bam, filter = FALSE, parallel = FALSE, plotMAPQ = FALSE, ...)

Arguments

bam	a BAM filename, or DataFrame/SummarizedExperiment with $BAM
filter	filter on bam$mtCovg? (default is FALSE, don't filter)
parallel	load multiple BAMs in parallel, if possible? (FALSE)
plotMAPQ	plot distribution of mitochondrial mapping quality? (FALSE)
...	additional args to pass scanBamParam(), such as mapqFilter

Value

an MAlignments or MAlignmentsList object

Examples

library(MTseekerData)
BAMdir <- system.file("extdata", "BAMs", package="MTseekerData")
BAMs <- paste0(BAMdir, "/", list.files(BAMdir, pattern=".bam$"))
(mal <- getMT(BAMs[1]))
class(mal) 

targets <- data.frame(BAM=BAMs, stringsAsFactors=FALSE) 
rownames(targets) <- sapply(strsplit(basename(BAMs), "\\."), `[`, 1)
(mall <- getMT(targets))
class(mall) 

MTseeker documentation built on Oct. 31, 2019, 3:20 a.m.