injectMTVariants: Inject (one or more) variants against rCRS.

In MTseeker: Bioconductor Tools for Human Mitochondrial Variant Analysis

Description

FIXME: this function could most likely be orders of magnitude faster. FIXME: this ONLY considers variants injected against rCRS, not RSRS or hg19.

Usage

injectMTVariants(mvr, gr = NULL, aa = TRUE, canon = 0.99, refX = 1,
  altX = 1)

Arguments

mvr	An MVRanges, usually from callMT, often subsetted
gr	A GRanges, usually of protein-coding regions (the default)
aa	Attempt to translate codon(s) affected by variant(s)? (TRUE)
canon	Minimum VAF to treat variants as canonical by subject (0.99)
refX	Reference depth below which variant is deemed canonical (1)
altX	Alternative depth above which variants deemed canonical (1)

Value

The GRanges, with ref/var DNA and AA and

Examples

library(MTseekerData)
RO_2 <- RONKSvariants[["RO_2"]]
injectMTVariants(RO_2)

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