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

Documentation for package ‘Rsamtools’ version 1.14.2

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

'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, filter, sort, and merge 'BAM' (binary alignment) files.
asBam-method	Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
asBcf	Operations on 'BCF' files.
asBcf-method	Operations on 'BCF' files.
asMates	Maintain and use BAM files
asMates-method	Maintain and use BAM files
asMates<-	Maintain and use BAM files
asMates<--method	Maintain and use BAM files

-- B --

bamDirname<-	Views into a set of BAM files
bamExperiment	Views into a set of BAM files
BamFile	Maintain and use BAM files
BamFile-class	Maintain and use BAM files
BamFileList	Maintain and use BAM files
BamFileList-class	Maintain and use 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
BamSampler	Sample from a BAM files
BamSampler-class	Sample from a 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 files.
BcfFile-class	Manipulate BCF files.
BcfFileList	Manipulate BCF files.
BcfFileList-class	Manipulate BCF files.
bcfFixed	Parameters for scanning BCF files
bcfGeno	Parameters for scanning BCF files
bcfInfo	Parameters for scanning BCF files
bcfMode	Manipulate BCF files.
bcfSamples	Parameters for scanning BCF files
bcfTrimEmpty	Parameters for scanning BCF files
bcfWhich	Parameters for scanning BCF files
bgzip	File compression for tabix (bgzip) and fasta (razip) files.
bzfile-class	'samtools' aligned sequence utilities interface

-- C --

close.BamFile	Maintain and use BAM files
close.BcfFile	Manipulate BCF 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, filter, sort, and merge 'BAM' (binary alignment) files.
countBam-method	Maintain and use BAM files
countBam-method	Views into a set of BAM files
countBam-method	Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
countDumpedAlignments	Pairing the elements of a GAlignments object
countFa	Operations on indexed 'fasta' files.
countFa-method	Manipulate indexed fasta files.
countFa-method	Operations on indexed 'fasta' files.
countTabix	Manipulate tabix indexed tab-delimited files.
coverage-method	Maintain and use BAM 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, filter, sort, and merge 'BAM' (binary alignment) files.
filterBam-method	Maintain and use BAM files
filterBam-method	Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
findMateAlignment	Pairing the elements of a GAlignments object
findMateAlignment2	Pairing the elements of a GAlignments object
findSpliceOverlaps-method	Maintain and use BAM files
FLAG_BITNAMES	Parameters for scanning BAM files
flushDumpedAlignments	Pairing the elements of a GAlignments object

-- G --

getDumpedAlignments	Pairing the elements of a GAlignments object
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, filter, sort, and merge 'BAM' (binary alignment) files.
indexBam-method	Maintain and use BAM files
indexBam-method	Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
indexBcf	Operations on 'BCF' files.
indexBcf-method	Manipulate BCF files.
indexBcf-method	Operations on 'BCF' 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.
isIncomplete-method	Maintain and use BAM files
isOpen-method	Maintain and use BAM files
isOpen-method	Manipulate BCF 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.

-- M --

makeGAlignmentPairs	Pairing the elements of a GAlignments object
makeGappedAlignmentPairs	Pairing the elements of a GAlignments object
mergeBam	Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
mergeBam-method	Maintain and use BAM files
mergeBam-method	Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.

-- N --

names-method	Views into a set of BAM files
names-method	A base class for managing lists of Rsamtools file references
names<--method	Views into a set of BAM files

-- O --

obeyQname	Maintain and use BAM files
obeyQname-method	Maintain and use BAM files
obeyQname<-	Maintain and use BAM files
obeyQname<--method	Maintain and use BAM files
open.BamFile	Maintain and use BAM files
open.BcfFile	Manipulate BCF 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

-- Q --

quickCountBam	Group the records of a BAM file based on their flag bits and count the number of records in each group
quickCountBam-method	Maintain and use BAM files
quickCountBam-method	Group the records of a BAM file based on their flag bits and count the number of records in each group

-- R --

razip	File compression for tabix (bgzip) and fasta (razip) files.
readBamGAlignmentsList	Reading a GAlignments, GappedReads, GAlignmentPairs, or GAlignmentsList object from a BAM file
readBamGappedAlignmentPairs	Reading a GAlignments, GappedReads, GAlignmentPairs, or GAlignmentsList object from a BAM file
readBamGappedAlignments	Reading a GAlignments, GappedReads, GAlignmentPairs, or GAlignmentsList object from a BAM file
readBamGappedReads	Reading a GAlignments, GappedReads, GAlignmentPairs, or GAlignmentsList object from a BAM file
readGAlignmentPairsFromBam	Reading a GAlignments, GappedReads, GAlignmentPairs, or GAlignmentsList object from a BAM file
readGAlignmentPairsFromBam-method	Maintain and use BAM files
readGAlignmentPairsFromBam-method	Reading a GAlignments, GappedReads, GAlignmentPairs, or GAlignmentsList object from a BAM file
readGAlignmentsFromBam	Reading a GAlignments, GappedReads, GAlignmentPairs, or GAlignmentsList object from a BAM file
readGAlignmentsFromBam-method	Maintain and use BAM files
readGAlignmentsFromBam-method	Views into a set of BAM files
readGAlignmentsFromBam-method	Reading a GAlignments, GappedReads, GAlignmentPairs, or GAlignmentsList object from a BAM file
readGAlignmentsListFromBam	Reading a GAlignments, GappedReads, GAlignmentPairs, or GAlignmentsList object from a BAM file
readGAlignmentsListFromBam-method	Maintain and use BAM files
readGAlignmentsListFromBam-method	Reading a GAlignments, GappedReads, GAlignmentPairs, or GAlignmentsList object from a BAM file
readGappedReadsFromBam	Reading a GAlignments, GappedReads, GAlignmentPairs, or GAlignmentsList object from a BAM file
readGappedReadsFromBam-method	Maintain and use BAM files
readGappedReadsFromBam-method	Reading a GAlignments, GappedReads, GAlignmentPairs, or GAlignmentsList object 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, filter, sort, and merge 'BAM' (binary alignment) files.
scanBam-method	Maintain and use BAM files
scanBam-method	Sample from a BAM files
scanBam-method	Views into a set of BAM files
scanBam-method	Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
scanBamFlag	Parameters for scanning BAM files
scanBamHeader	Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
scanBamHeader-method	Maintain and use BAM files
scanBamHeader-method	Import, count, index, filter, sort, and merge '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 'BCF' files.
scanBcf-method	Manipulate BCF files.
scanBcf-method	Operations on 'BCF' files.
scanBcfHeader	Operations on 'BCF' files.
scanBcfHeader-method	Manipulate BCF files.
scanBcfHeader-method	Operations on 'BCF' files.
ScanBcfParam	Parameters for scanning BCF files
ScanBcfParam-class	Parameters for scanning BCF files
ScanBcfParam-method	Parameters for scanning BCF files
ScanBVcfParam-class	Parameters for scanning 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.
seqinfo-method	Maintain and use BAM files
seqinfo-method	Manipulate indexed fasta 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.
sequenceLayer	Lay read sequences alongside the reference space, using their CIGARs
show-method	Maintain and use BAM files
show-method	Sample from a BAM files
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 BCF files
sortBam	Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
sortBam-method	Maintain and use BAM files
sortBam-method	Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
stackStringsFromBam	Stack the read sequences stored in a BAM file on a region of interest
summarizeOverlaps-method	Maintain and use 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 --

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

-- Y --

yieldSize	A base class for managing file references in Rsamtools
yieldSize-method	A base class for managing file references in Rsamtools
yieldSize-method	A base class for managing lists of Rsamtools file references
yieldSize<-	A base class for managing file references in Rsamtools
yieldSize<--method	A base class for managing file references in Rsamtools
yieldSize<--method	A base class for managing lists of Rsamtools file references
yieldTabix	Deprecated functions
yieldTabix-method	Deprecated functions

-- misc --

[-method

Views into a set of BAM files