importVCF: Import a VCF directly into MTseeker

In trichelab/MTseeker: Bioconductor Tools for Human Mitochondrial Variant Analysis

Description

Import a VCF directly into MTseeker

Usage

importVCF(x, gzip = TRUE, biscuit = FALSE, verbose = TRUE)

Arguments

x	character, list or dataframe for file name of VCF(and BAM)
gzip	Is the input gzipped? (FIXME: autodetect this)
biscuit	Is the input VCF from biscuit? (FALSE)
verbose	Print all messages during progress? (TRUE)

Value

an MVRangesList

Examples

library(MTseekerData)
VCFdir <- system.file("extdata", package="MTseekerData")
VCF <- file.path(VCFdir, list.files(VCFdir, pattern="*.vcf.gz$"))
mvr <- importVCF(VCF)[[1]]
mvr$FILTER <- ifelse(totalDepth(mvr) >= 20, "PASS", ".")
mvr$PASS <- mvr$FILTER == "PASS"
filterMT(mvr)

trichelab/MTseeker documentation built on March 8, 2021, 6:20 p.m.