Import aligned BAM file format sequences into R / Bioconductor


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Documentation for package ‘Rsamtools’ version 1.4.3

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A B C D F G I N O P R S U misc

Rsamtools-package 'samtools' aligned sequence utilities interface

-- A --

asBam Import, count, index, and other operations on 'BAM' (binary alignment) files.
asBam-method Import, count, index, and other operations on 'BAM' (binary alignment) files.

-- B --

bamDirname<- Views into a set of BAM files
bamExperiment Views into a set of BAM files
BamFile Maintain SAM and BAM files
BamFile-class Maintain SAM and 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
BcfFile Manipulate BCF or VCF files.
BcfFile-class Manipulate BCF or VCF files.
bcfGeno Parameters for scanning VCF / BCF files
bcfInfo Parameters for scanning VCF / BCF files
bcfMode Manipulate BCF or VCF files.
bcfTrimEmpty Parameters for scanning VCF / BCF files
bcfWhich Parameters for scanning VCF / BCF files
bzfile-class 'samtools' aligned sequence utilities interface

-- C --

close.BamFile Maintain SAM and BAM files
close.BcfFile Manipulate BCF or VCF files.
close.FaFile Manipulate indexed fasta files.
countBam Import, count, index, and other operations on 'BAM' (binary alignment) files.
countBam-method Maintain SAM and BAM files
countBam-method Views into a set of BAM files
countBam-method Import, count, index, and other operations on 'BAM' (binary alignment) files.
countFa Operations on indexed 'fasta' files.
countFa-method Manipulate indexed fasta files.
countFa-method Operations on indexed 'fasta' files.

-- D --

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

-- F --

FaFile Manipulate indexed fasta files.
FaFile-class Manipulate indexed fasta files.
fifo-class 'samtools' aligned sequence utilities interface
filterBam Import, count, index, and other operations on 'BAM' (binary alignment) files.
filterBam-method Maintain SAM and BAM files
filterBam-method Import, count, index, and other operations on 'BAM' (binary alignment) files.

-- G --

gzfile-class 'samtools' aligned sequence utilities interface

-- I --

index A base class for managing file references in Rsamtools
indexBam Import, count, index, and other operations on 'BAM' (binary alignment) files.
indexBam-method Maintain SAM and BAM files
indexBam-method Import, count, index, and other operations on 'BAM' (binary alignment) files.
indexFa Operations on indexed 'fasta' files.
indexFa-method Manipulate indexed fasta files.
indexFa-method Operations on indexed 'fasta' files.
isOpen-method Maintain SAM and BAM files
isOpen-method Manipulate BCF or VCF files.
isOpen-method Manipulate indexed fasta files.
isOpen-method A base class for managing file references in Rsamtools

-- N --

names-method Views into a set of BAM files
names<--method Views into a set of BAM files

-- O --

open.BamFile Maintain SAM and BAM files
open.BcfFile Manipulate BCF or VCF files.
open.FaFile Manipulate indexed fasta files.

-- P --

path A base class for managing file references in Rsamtools
pipe-class 'samtools' aligned sequence utilities interface

-- R --

readBamGappedAlignments GappedAlignments objects
readBamGappedAlignments-method Maintain SAM and BAM files
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
RsamtoolsFile-class A base class for managing file references in Rsamtools

-- S --

scanBam Import, count, index, and other operations on 'BAM' (binary alignment) files.
scanBam-method Maintain SAM and BAM 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 Maintain SAM and BAM 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
scanBcf Operations on 'VCF' or 'BCF' (variant call) files.
scanBcf-method Manipulate BCF or VCF files.
scanBcf-method Operations on 'VCF' or 'BCF' (variant call) files.
scanBcfHeader Operations on 'VCF' or 'BCF' (variant call) files.
scanBcfHeader-method Manipulate BCF or VCF files.
scanBcfHeader-method Operations on 'VCF' or 'BCF' (variant call) files.
ScanBcfParam Parameters for scanning VCF / BCF files
ScanBcfParam-class Parameters for scanning VCF / BCF files
ScanBcfParam-method Parameters for scanning VCF / BCF files
scanFa Operations on indexed 'fasta' files.
scanFa-method Manipulate indexed fasta files.
scanFa-method Operations on indexed 'fasta' files.
scanFaIndex Operations on indexed 'fasta' files.
scanFaIndex-method Manipulate indexed fasta files.
scanFaIndex-method Operations on indexed 'fasta' files.
show-method Views into a set of BAM files
show-method A base class for managing file references in Rsamtools
show-method Parameters for scanning BAM files
show-method Parameters for scanning VCF / BCF files
sortBam Import, count, index, and other operations on 'BAM' (binary alignment) files.
sortBam-method Maintain SAM and BAM files
sortBam-method Import, count, index, and other operations on 'BAM' (binary alignment) files.

-- U --

unz-class 'samtools' aligned sequence utilities interface
url-class 'samtools' aligned sequence utilities interface

-- misc --

[-method Views into a set of BAM files