decomposeAndCalcConsequences: Decompose and annotate AA changes in MT variants

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

Description

FIXME: this function is remarkably slow

Usage

decomposeAndCalcConsequences(mvr, coding = TRUE, AAchanges = TRUE, ...)

Arguments

mvr	An MVRangesList or MVRanges object
coding	Annotate only coding regions? (TRUE)
AAchanges	Annotate amino acid (AA) changes? (TRUE)
...	Other arguments to pass to injectMTVariants

Value

       Annotated variants, as an MVRanges

Examples

library(MTseekerData)
library(VariantTools)

# Set a really high depth filter
# Just an example, not something you'd use to filter real data
# Something like 20 reads is more reasonable (gives Sanger-like error rates)
filters <- 
  FilterRules(list(minTotalDepth=MinTotalDepthFilter(min.depth=2e3L)))
ronks_vars.anno <- subsetByFilter(RONKSvariants[[1]], filters)
decomposeAndCalcConsequences(ronks_vars.anno)

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