MVRangesList-methods: Wrap a VRangesList for mitochondrial use.

In MTseeker: Bioconductor Tools for Human Mitochondrial Variant Analysis

Description

Usually an MVRangesList will be created by callMT.

Usage

MVRangesList(...)

## 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
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

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 '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")
BAMs <- paste0(BAMdir, "/", list.files(BAMdir, pattern=".bam$"))
targets <- data.frame(BAM=BAMs, stringsAsFactors=FALSE) 
rownames(targets) <- sapply(strsplit(basename(BAMs), "\\."), `[`, 1)
(mall <- getMT(targets))

if (requireNamespace("GmapGenome.Hsapiens.rCRS", quietly=TRUE)) {
  (mvrl <- callMT(mall))
  filt(mvrl$pt1_cell1)
} else { 
  message("You have not yet installed an rCRS reference genome.")
  message("Consider running the indexMTgenome() function to do so.")
  message("An example MVRangesList is RONKSvariants from MTseekerData.")
}

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