callMT: call mitochondrial variants against rCRS from an...

In MTseeker: Bioconductor Tools for Human Mitochondrial Variant Analysis

Description

'callMTVars' is a helper function for callMT

Usage

callMT(mal, ..., parallel = FALSE, verbose = FALSE)

callMTVars(BAM, SIZE = 75, GENOME = "rCRS", CHR = "chrM",
  COV = NULL, verbose = FALSE)

Arguments

mal	an MAlignments (or, potentially, an MAlignmentsList)
...	other arguments to pass to VariantTools::callVariants
parallel	try to run in parallel? (FALSE; this is super unstable)
verbose	be verbose? (FALSE; turn on for debugging purposes)
BAM	the BAM filename (for callMTVars)
SIZE	the read length (for callMTVars; default is 75)
GENOME	the reference genome (for callMTVars; default is rCRS)
CHR	the mt contig name (for callMTVars; default is chrM)
COV	average read coverage (so we don't have to countBam)

Details

FIXME: transition gmapR from import to suggestion FIXME: use Rsamtools::pileup by default FIXME: optional haplogroup masking?

Value

an MVRanges (or, potentially, an MVRangesList)

Examples

library(MTseekerData)
BAMdir <- system.file("extdata", "BAMs", package="MTseekerData")
BAMs <- paste0(BAMdir, "/", list.files(BAMdir, pattern=".bam$"))
(mal <- getMT(BAMs[1]))
if (requireNamespace("GmapGenome.Hsapiens.rCRS", quietly=TRUE)) {
  (mvr <- callMT(mal))
  filt(snpCall(mvr))
} else { 
  message("You have not yet installed an rCRS reference genome.")
  message("Consider running the indexMTgenome() function to do so.")
  message("The RONKSvariants object in MTseekerData is a result of callMT.")
}

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