Binary alignment (BAM), variant call (BCF), or tabix file import


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Documentation for package ‘Rsamtools’ version 1.6.3

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A B C D F G H I N O P R S T U V Y misc

Rsamtools-package 'samtools' aligned sequence utilities interface

-- A --

applyPileups Create summary pile-up statistics across multiple BAM files.
applyPileups-method Represent BAM files for pileup summaries.
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.
asBcf Operations on 'VCF' or 'BCF' (variant call) files.
asBcf-method Operations on 'VCF' or 'BCF' (variant call) 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
BamFileList Maintain SAM and BAM files
BamFileList-class Maintain SAM and BAM files
bamFlag Parameters for scanning BAM files
bamFlag<- Parameters for scanning BAM files
bamFlagAND Parameters for scanning BAM files
bamFlagAsBitMatrix Parameters for scanning BAM files
bamFlagTest 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
bamWhich<--method Parameters for scanning BAM files
BcfFile Manipulate BCF or VCF files.
BcfFile-class Manipulate BCF or VCF files.
BcfFileList Manipulate BCF or VCF files.
BcfFileList-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
bgzip File compression for tabix (bgzip) and fasta (razip) files.
bgzipTabix File compression for tabix (bgzip) and fasta (razip) 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.
close.PileupFiles Represent BAM files for pileup summaries.
close.RsamtoolsFileList A base class for managing lists of Rsamtools file references
close.TabixFile Manipulate tabix indexed tab-delimited 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.
FaFileList Manipulate indexed fasta files.
FaFileList-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 --

getSeq-method Manipulate indexed fasta files.
gzfile-class 'samtools' aligned sequence utilities interface

-- H --

headerTabix Retrieve sequence names defined in a tabix file.
headerTabix-method Manipulate tabix indexed tab-delimited files.
headerTabix-method Retrieve sequence names defined in a tabix file.

-- 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.
indexBcf Operations on 'VCF' or 'BCF' (variant call) files.
indexBcf-method Manipulate BCF or VCF files.
indexBcf-method Operations on 'VCF' or 'BCF' (variant call) files.
indexFa Operations on indexed 'fasta' files.
indexFa-method Manipulate indexed fasta files.
indexFa-method Operations on indexed 'fasta' files.
indexTabix Compress and index tabix-compatible files.
isOpen-method Maintain SAM and BAM files
isOpen-method Manipulate BCF or VCF files.
isOpen-method Manipulate indexed fasta files.
isOpen-method Represent BAM files for pileup summaries.
isOpen-method A base class for managing file references in Rsamtools
isOpen-method A base class for managing lists of Rsamtools file references
isOpen-method Manipulate tabix indexed tab-delimited files.

-- 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.
open.PileupFiles Represent BAM files for pileup summaries.
open.RsamtoolsFileList A base class for managing lists of Rsamtools file references
open.TabixFile Manipulate tabix indexed tab-delimited files.

-- P --

path A base class for managing file references in Rsamtools
path-method A base class for managing file references in Rsamtools
path-method A base class for managing lists of Rsamtools file references
PileupFiles Represent BAM files for pileup summaries.
PileupFiles-class Represent BAM files for pileup summaries.
PileupFiles-method Represent BAM files for pileup summaries.
PileupParam Parameters for creating pileups from BAM files
PileupParam-class Parameters for creating pileups from BAM files
pipe-class 'samtools' aligned sequence utilities interface
plpFiles Represent BAM files for pileup summaries.
plpFlag Parameters for creating pileups from BAM files
plpFlag<- Parameters for creating pileups from BAM files
plpMaxDepth Parameters for creating pileups from BAM files
plpMaxDepth<- Parameters for creating pileups from BAM files
plpMinBaseQuality Parameters for creating pileups from BAM files
plpMinBaseQuality<- Parameters for creating pileups from BAM files
plpMinDepth Parameters for creating pileups from BAM files
plpMinDepth<- Parameters for creating pileups from BAM files
plpMinMapQuality Parameters for creating pileups from BAM files
plpMinMapQuality<- Parameters for creating pileups from BAM files
plpParam Represent BAM files for pileup summaries.
plpWhat Parameters for creating pileups from BAM files
plpWhat<- Parameters for creating pileups from BAM files
plpWhich Parameters for creating pileups from BAM files
plpWhich<- Parameters for creating pileups from BAM files
plpYieldAll Parameters for creating pileups from BAM files
plpYieldAll<- Parameters for creating pileups from BAM files
plpYieldBy Parameters for creating pileups from BAM files
plpYieldBy<- Parameters for creating pileups from BAM files
plpYieldSize Parameters for creating pileups from BAM files
plpYieldSize<- Parameters for creating pileups from BAM files

-- R --

razip File compression for tabix (bgzip) and fasta (razip) files.
readBamGappedAlignments Reading GappedAlignments or GappedReads objects from a BAM file
readBamGappedAlignments-method Maintain SAM and BAM files
readBamGappedAlignments-method Views into a set of BAM files
readBamGappedAlignments-method Reading GappedAlignments or GappedReads objects from a BAM file
readBamGappedReads Reading GappedAlignments or GappedReads objects from a BAM file
readBamGappedReads-method Maintain SAM and BAM files
readBamGappedReads-method Reading GappedAlignments or GappedReads objects from a BAM file
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
RsamtoolsFileList A base class for managing lists of Rsamtools file references
RsamtoolsFileList-class A base class for managing lists of Rsamtools file references

-- 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
ScanBVcfParam-class 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.
scanTabix Operations on 'tabix' (indexed, tab-delimited) files.
scanTabix-method Manipulate tabix indexed tab-delimited files.
scanTabix-method Operations on 'tabix' (indexed, tab-delimited) files.
scanVcf Operations on 'VCF' or 'BCF' (variant call) files.
scanVcf-method Manipulate tabix indexed tab-delimited files.
scanVcf-method Operations on 'VCF' or 'BCF' (variant call) files.
scanVcfHeader Operations on 'VCF' or 'BCF' (variant call) files.
scanVcfHeader-method Manipulate tabix indexed tab-delimited files.
scanVcfHeader-method Operations on 'VCF' or 'BCF' (variant call) files.
ScanVcfParam Parameters for scanning VCF / BCF files
ScanVcfParam-class Parameters for scanning VCF / BCF files
ScanVcfParam-method Parameters for scanning VCF / BCF files
seqinfo-method Maintain SAM and BAM files
seqnamesTabix Retrieve sequence names defined in a tabix file.
seqnamesTabix-method Manipulate tabix indexed tab-delimited files.
seqnamesTabix-method Retrieve sequence names defined in a tabix file.
show-method Views into a set of BAM files
show-method Represent BAM files for pileup summaries.
show-method Parameters for creating pileups from 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.
summarizeOverlaps-method Maintain SAM and BAM files
summarizeOverlaps-method Views into a set of BAM files

-- T --

TabixFile Manipulate tabix indexed tab-delimited files.
TabixFile-class Manipulate tabix indexed tab-delimited files.
TabixFileList Manipulate tabix indexed tab-delimited files.
TabixFileList-class Manipulate tabix indexed tab-delimited files.

-- U --

unpackVcf Operations on 'VCF' or 'BCF' (variant call) files.
unpackVcf-method Operations on 'VCF' or 'BCF' (variant call) files.
unz-class 'samtools' aligned sequence utilities interface
url-class 'samtools' aligned sequence utilities interface

-- V --

vcfGeno Parameters for scanning VCF / BCF files
vcfInfo Parameters for scanning VCF / BCF files
vcfTrimEmpty Parameters for scanning VCF / BCF files
vcfWhich Parameters for scanning VCF / BCF files

-- Y --

yieldTabix Yield records from a stream of records contained in a tabix file.
yieldTabix-method Manipulate tabix indexed tab-delimited files.

-- misc --

[-method Views into a set of BAM files