MVRanges-methods: wrap a VRanges for mitochondrial use

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

Description

Usually the MVRanges constructor will be called by callMT().

Many of these methods can be dispatched from an MVRangesList OR an MVRanges. In such cases, the method will usually, but not always, be apply()ed.

Usage

MVRanges(vr = NULL, coverage = NA_real_)

## S4 method for signature 'MVRanges'
genomeCoverage(x)

## S4 method for signature 'MVRanges'
coverage(x)

## S4 method for signature 'MVRanges'
type(x)

## S4 method for signature 'MVRanges'
genes(x)

## S4 method for signature 'MVRanges'
snpCall(object)

## S4 method for signature 'MVRanges'
pos(x)

## S4 method for signature 'MVRanges'
show(object)

## S4 method for signature 'MVRanges'
annotation(object)

## S4 method for signature 'MVRanges'
getAnnotations(annotations)

## S4 method for signature 'MVRanges'
encoding(x)

## S4 method for signature 'MVRanges'
filt(x)

## S4 method for signature 'MVRanges'
genome(x)

## S4 method for signature 'MVRanges,missing,missing'
locateVariants(query, filterLowQual = FALSE, ...)

## S4 method for signature 'MVRanges,missing,missing,missing'
predictCoding(query, subject, seqSource, varAllele, ...)

## S4 method for signature 'MVRanges,missing,missing'
summarizeVariants(query, subject, mode, ...)

## S4 method for signature 'MVRanges,ANY'
plot(x, y, ...)

## S4 method for signature 'MVRanges'
consensusString(x, ...)

Arguments

vr	the VRanges
coverage	estimated coverage
x	an MVRanges
object	an MVRanges
annotations	an MVRanges
query	an MVRanges
filterLowQual	boolean; drop non-PASSing variants from locateVariants?
...	miscellaneous args, passed through
subject	a GRanges, usually
seqSource	a BSgenome, usually
varAllele	variant alleles
mode	miscellaneous arguments
y	another MVRanges

Value

       an MVRanges

         depends on the method invoked.

Utility methods

pos returns a character vector describing variant positions. filt returns a subset of variant calls where PASS == TRUE (i.e. filtered) coverage returns an Rle of coverage across the mitochondrial genome genomeCoverage returns the estimated mitochondrial read coverage depth

Annotation methods

type returns a character vector describing variant type (SNV or indel) genes retrieves a GRanges of mitochondrial gene locations for an MVRanges snpCall retrieves single nucleotide variant polymorphisms PASSing filters annotation gets (perhaps oddly) an MVRanges object annotated against rCRS getAnnotations returns the GRanges of gene/region annotations for an MVR encoding returns variants residing in coding regions (consequence unknown) locateVariants annotates variants w/region, gene, and localStart/localEnd predictCoding returns variants consequence predictions as one might expect summarizeVariants uses MitImpact to attempt annotation of coding variants. consensusString edits rCRS to create a consensus genotype for eg Haplogrep

Visualization methods

plot creates a circular plot of mitochondrial variant calls with annotation

Examples

library(MTseekerData)
BAMdir <- system.file("extdata", "BAMs", package="MTseekerData")
BAMs <- paste0(BAMdir, "/", list.files(BAMdir, pattern="^pt.*bam$"))
(mvr <- filterMTvars(pileupMT(BAMs[1], ref="rCRS")))
locateVariants(head(encoding(mvr))) # FIXME: no gene overlaps?!?
predictCoding(mvr) # FIXME: none!

# summarizeVariants can take a LONG time to run, and requires Internet

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