Import aligned BAM file format sequences into R / Bioconductor


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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