MAlignmentsList-methods: wrap a GAlignmentsList for viewing

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

Description

Normally the MAlignmentsList constructor will be called by getMT.

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 MAlignmentsList as their argument.

Usage

MAlignmentsList(...)

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

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

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

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

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

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

Arguments

...	MAlignments
object	an MAlignmentsList
files	an MAlignmentsList
x	an MAlignmentsList

Value

       an MAlignments 

     various objects, as appropriate to the method 

Examples

library(MTseekerData)
BAMdir <- system.file("extdata", "BAMs", package="MTseekerData")
print(BAMdir)
BAMs <- paste0(BAMdir, "/", list.files(BAMdir, pattern=".bam$"))
print(BAMs)
mall <- getMT(BAMs[1]) # a xenograft
genomeLength(mall) 
readLength(mall) 
fileName(mall) 
scanBamHeader(mall) 

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