MVRangesList-methods: Wrap a VRangesList for mitochondrial use.

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

Description

Usually an MVRangesList will be created by callMT.

Usage

MVRangesList(..., bamFiles = NULL, coverageRles = NULL, verbose = FALSE)

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

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

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

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

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

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

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

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

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

## S4 method for signature 'MVRangesList'
granges(x, filterLowQual = TRUE)

## S4 method for signature 'MVRangesList,missing,missing'
summarizeVariants(query, filterLowQual = TRUE, ...)

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

## S4 method for signature 'MVRangesList,missing,missing'
locateVariants(query, filterLowQual = TRUE, ...)

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

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

Arguments

...	miscellaneous args, passed through
bamFiles	(Optional) BAM filenames for each MVRanges element
coverageRles	(Optional) coverage Rles for each MVRanges element
verbose	Be verbose? (default is FALSE)
x	an MVRangesList (for some methods)
object	an MVRangesList (for other methods)
annotations	an MVRangesList (for getAnnotations)
query	an MVRangesList (for predictCoding)
subject	a GRanges, usually
seqSource	a BSgenome, usually
varAllele	variant alleles
filterLowQual	opt. for granges/summarizeVariants
y	another MVRangesList

Details

If the elements were generated by pileupMT(), a coverageRles DataFrame will be generated and placed into the metadata() list for the result. Similarly, if an element named 'bam' is located in the metadata of the supplied arguments, it will be combined into a vector named bamFiles.

Value

           the MVRangesList

         depends on the method invoked.

Utility methods

genomeCoverage returns estimated mitochondrial read coverage depth coverage returns an RleList of coverage for each sample's chrM filt removes variants where PASS != TRUE for each element

Annotation methods

genes returns an annotated GRanges of mitochondrial genes metadata get or set elements in the metadata() of an MVRL getAnnotations returns a GRanges of annotated mitochondrial features genome returns the genome (or, perhaps, genomes) in an MVRL encoding returns mutations in coding regions for each element granges returns mildly annotated aggregates of variant sites snpCall retrieves single nucleotide variant polymorphisms locateVariants locates variants within genes, tRNA, rRNA, or D-loop summarizeVariants attempts mass functional annotation of variant sites consensusString creates consensus genotypes from rCRS for eg Haplogrep

Visualization methods

plot creates circular plot of mitochondrial variant calls

Examples

library(MTseekerData)
BAMdir <- system.file("extdata", "BAMs", package="MTseekerData")
pdxBAMs <- paste0(BAMdir, "/", list.files(BAMdir, pattern="^PDX.*.bam$"))
(mvrl <- pileupXenograft(pdxBAMs[1]))

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