MAlignmentsList-methods: wrap a GAlignmentsList for viewing

In 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'
genomeCoverage(x)

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

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

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

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

Arguments

...	MAlignments
x	an MAlignmentsList
object	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)
targets <- data.frame(BAM=BAMs, stringsAsFactors=FALSE) 
rownames(targets) <- sapply(strsplit(basename(BAMs), "\\."), `[`, 1)
mall <- getMT(targets)
class(mall) 
show(mall) 

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