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

Documentation for package ‘Rsamtools’ version 2.10.0

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

'samtools' aligned sequence utilities interface

-- A --

applyPileups	Apply a user-provided function to calculate pile-up statistics across multiple BAM files.
applyPileups-method	Represent BAM files for pileup summaries.
ApplyPileupsParam	Parameters for creating pileups from BAM files
ApplyPileupsParam-class	Parameters for creating pileups from BAM files
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
asSam	Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
asSam-method	Import, count, index, filter, sort, and merge 'BAM' (binary alignment) 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
bamMapqFilter	Parameters for scanning BAM files
bamMapqFilter<-	Parameters for scanning 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	Deprecated functions
BamSampler-class	Deprecated functions
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
bamTagFilter	Parameters for scanning BAM files
bamTagFilter<-	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. IMPORTANT NOTE: Starting with Rsamtools 1.99.0 (Bioconductor 3.9), 'razip()' is defunct. Please use 'bgzip()' instead.
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.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.
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.
cycle_bins	Use filters and output formats to calculate pile-up statistics for a BAM file.

-- 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
distinguish_nucleotides	Use filters and output formats to calculate pile-up statistics for a BAM file.
distinguish_strands	Use filters and output formats to calculate pile-up statistics for a BAM file.

-- 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.
FLAG_BITNAMES	Parameters for scanning BAM files

-- G --

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

-- H --

hasUnmappedMate	Parameters for scanning BAM files
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 --

idxstatsBam	Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
idxstatsBam-method	Maintain and use BAM files
idxstatsBam-method	Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
ignore_query_Ns	Use filters and output formats to calculate pile-up statistics for a BAM file.
include_deletions	Use filters and output formats to calculate pile-up statistics for a BAM file.
include_insertions	Use filters and output formats to calculate pile-up statistics for a BAM file.
index	A base class for managing file references in Rsamtools
index-method	A base class for managing file references in Rsamtools
index-method	A base class for managing lists of Rsamtools file references
index<-	A base class for managing file references in Rsamtools
index<--method	A base class for managing file references in Rsamtools
index<--method	A base class for managing lists of Rsamtools file references
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.
isDuplicate	Parameters for scanning BAM files
isFirstMateRead	Parameters for scanning BAM files
isIncomplete-method	Maintain and use BAM files
isMateMinusStrand	Parameters for scanning BAM files
isMinusStrand	Parameters for scanning BAM files
isNotPassingQualityControls	Parameters for scanning BAM files
isNotPrimaryRead	Parameters for scanning 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.
isPaired	Parameters for scanning BAM files
isProperPair	Parameters for scanning BAM files
isSecondaryAlignment	Parameters for scanning BAM files
isSecondMateRead	Parameters for scanning BAM files
isUnmappedQuery	Parameters for scanning BAM files

-- L --

left_bins

Use filters and output formats to calculate pile-up statistics for a BAM file.

-- M --

max_depth	Use filters and output formats to calculate pile-up statistics for a BAM file.
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.
min_base_quality	Use filters and output formats to calculate pile-up statistics for a BAM file.
min_mapq	Use filters and output formats to calculate pile-up statistics for a BAM file.
min_minor_allele_depth	Use filters and output formats to calculate pile-up statistics for a BAM file.
min_nucleotide_depth	Use filters and output formats to calculate pile-up statistics for a BAM file.

-- 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.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
phred2ASCIIOffset	Use filters and output formats to calculate pile-up statistics for a BAM file.
pileup	Use filters and output formats to calculate pile-up statistics for a BAM file.
pileup-method	Use filters and output formats to calculate pile-up statistics for a BAM file.
PileupFiles	Represent BAM files for pileup summaries.
PileupFiles-class	Represent BAM files for pileup summaries.
PileupFiles-method	Represent BAM files for pileup summaries.
PileupParam	Use filters and output formats to calculate pile-up statistics for a BAM file.
PileupParam-class	Use filters and output formats to calculate pile-up statistics for a BAM file.
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 --

qnamePrefixEnd	Maintain and use BAM files
qnamePrefixEnd-method	Maintain and use BAM files
qnamePrefixEnd<-	Maintain and use BAM files
qnamePrefixEnd<--method	Maintain and use BAM files
qnameSuffixStart	Maintain and use BAM files
qnameSuffixStart-method	Maintain and use BAM files
qnameSuffixStart<-	Maintain and use BAM files
qnameSuffixStart<--method	Maintain and use BAM files
query_bins	Use filters and output formats to calculate pile-up statistics for a BAM file.
quickBamFlagSummary	Group the records of a BAM file based on their flag bits and count the number of records in each group
quickBamFlagSummary-method	Maintain and use BAM files
quickBamFlagSummary-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. IMPORTANT NOTE: Starting with Rsamtools 1.99.0 (Bioconductor 3.9), 'razip()' is defunct. Please use 'bgzip()' instead.
readPileup	Import samtools 'pileup' files.
readPileup-method	Import samtools 'pileup' files.
Rsamtools	'samtools' aligned sequence utilities interface
RsamtoolsFile	A base class for managing file references in Rsamtools
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	Views into a set of BAM files
scanBam-method	Deprecated functions
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.
show-method	Parameters for creating pileups from BAM files
show-method	Maintain and use BAM files
show-method	Views into a set of BAM files
show-method	Manipulate indexed fasta files.
show-method	Represent BAM files for pileup summaries.
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
show-method	Deprecated functions
show-method	Use filters and output formats to calculate pile-up statistics for a BAM file.
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.

-- 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.
testPairedEndBam	Quickly test if a BAM file has paired end reads
testPairedEndBam-method	Quickly test if a BAM file has paired end reads

-- 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