MAlignments-methods: wrap a GAlignments for easier stats

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

Description

Normally the MAlignments constructor will be called by getMT(bam).

Depending on how a generic was originally designated, the arguments to these methods can have various argument names, but all of them tend to take an MAlignments as their argument.

Usage

MAlignments(gal, bam)

genomeCoverage(x)

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

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

## S4 method for signature 'MAlignments'
fileName(object)

## S4 method for signature 'MAlignments'
scanBamHeader(files)

readLength(x)

## S4 method for signature 'MAlignments'
readLength(x)

genomeLength(x)

## S4 method for signature 'MAlignments'
genomeLength(x)

Arguments

gal	a GAlignments
bam	a bam filename
x	an MAlignments
object	an MAlignments
files	an MAlignments

Value

       an MAlignments 

     various things, as appropriate to the methods

Examples

library(MTseekerData)
BAMdir <- system.file("extdata", "BAMs", package="MTseekerData")
patientBAMs <- paste0(BAMdir, "/", list.files(BAMdir, pattern="^pt.*.bam$"))
mal <- getMT(patientBAMs[1])
class(mal) 
show(mal) 

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