Import aligned BAM file format sequences into R / Bioconductor

Documentation for package ‘Rsamtools’ version 1.2.3

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Rsamtools-package	'samtools' aligned sequence utilities interface
bamDirname<-	Views into a set of BAM files
bamExperiment	Views into a set of BAM files
bamFlag	Parameters for scanning BAM files
bamFlag<-	Parameters for scanning BAM files
bamIndicies	Views into a set of BAM files
bamPaths	Views into a set of BAM files
bamRanges	Views into a set of BAM files
bamRanges<-	Views into a set of BAM files
bamReverseComplement	Parameters for scanning BAM files
bamReverseComplement<-	Parameters for scanning BAM files
bamSamples	Views into a set of BAM files
bamSamples<-	Views into a set of BAM files
bamSimpleCigar	Parameters for scanning BAM files
bamSimpleCigar<-	Parameters for scanning BAM files
bamTag	Parameters for scanning BAM files
bamTag<-	Parameters for scanning BAM files
BamViews	Views into a set of BAM files
BamViews-class	Views into a set of BAM files
BamViews-method	Views into a set of BAM files
bamWhat	Parameters for scanning BAM files
bamWhat<-	Parameters for scanning BAM files
bamWhich	Parameters for scanning BAM files
bamWhich<-	Parameters for scanning BAM files
countBam	Import, count, index, and other operations on 'BAM' (binary alignment) files.
countBam-method	Views into a set of BAM files
countBam-method	Import, count, index, and other operations on 'BAM' (binary alignment) files.
dim-method	Views into a set of BAM files
dimnames-method	Views into a set of BAM files
dimnames<--method	Views into a set of BAM files
filterBam	Import, count, index, and other operations on 'BAM' (binary alignment) files.
filterBam-method	Import, count, index, and other operations on 'BAM' (binary alignment) files.
indexBam	Import, count, index, and other operations on 'BAM' (binary alignment) files.
indexBam-method	Import, count, index, and other operations on 'BAM' (binary alignment) files.
names-method	Views into a set of BAM files
names<--method	Views into a set of BAM files
readBamGappedAlignments	GappedAlignments objects
readBamGappedAlignments-method	Views into a set of BAM files
readBamGappedAlignments-method	GappedAlignments objects
readPileup	Import samtools 'pileup' files.
readPileup-method	Import samtools 'pileup' files.
Rsamtools	'samtools' aligned sequence utilities interface
scanBam	Import, count, index, and other operations on 'BAM' (binary alignment) files.
scanBam-method	Views into a set of BAM files
scanBam-method	Import, count, index, and other operations on 'BAM' (binary alignment) files.
scanBamFlag	Parameters for scanning BAM files
scanBamHeader	Import, count, index, and other operations on 'BAM' (binary alignment) files.
scanBamHeader-method	Import, count, index, and other operations on 'BAM' (binary alignment) files.
ScanBamParam	Parameters for scanning BAM files
ScanBamParam-class	Parameters for scanning BAM files
ScanBamParam-method	Parameters for scanning BAM files
scanBamWhat	Parameters for scanning BAM files
show-method	Views into a set of BAM files
show-method	Parameters for scanning BAM files
sortBam	Import, count, index, and other operations on 'BAM' (binary alignment) files.
sortBam-method	Import, count, index, and other operations on 'BAM' (binary alignment) files.
[-method	Views into a set of BAM files