Import aligned BAM file format sequences into R / Bioconductor

Documentation for package ‘Rsamtools’ version 1.4.3

DESCRIPTION file.
Overview of user guides and package vignettes; browse directory.
Package NEWS.

Help Pages

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