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


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Documentation for package ‘Rsamtools’ version 1.12.4

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

-- 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.
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 GappedAlignments object
countFa Operations on indexed 'fasta' files.
countFa-method Manipulate indexed fasta files.
countFa-method Operations on indexed 'fasta' 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 GappedAlignments object
findMateAlignment2 Pairing the elements of a GappedAlignments object
findSpliceOverlaps-method Maintain and use BAM files
FLAG_BITNAMES Parameters for scanning BAM files
flushDumpedAlignments Pairing the elements of a GappedAlignments object

-- G --

getDumpedAlignments Pairing the elements of a GappedAlignments 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.
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 --

makeGappedAlignmentPairs Pairing the elements of a GappedAlignments 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 A base class for managing file references in Rsamtools
obeyQname-method A base class for managing file references in Rsamtools
obeyQname-method A base class for managing lists of Rsamtools file references
obeyQname<- A base class for managing file references in Rsamtools
obeyQname<--method A base class for managing file references in Rsamtools
obeyQname<--method A base class for managing lists of Rsamtools file references
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 BAM file into a GappedAlignments, GappedReads, or GappedAlignmentPairs object
readBamGAlignmentsList-method Maintain and use BAM files
readBamGAlignmentsList-method Reading a BAM file into a GappedAlignments, GappedReads, or GappedAlignmentPairs object
readBamGappedAlignmentPairs Reading a BAM file into a GappedAlignments, GappedReads, or GappedAlignmentPairs object
readBamGappedAlignmentPairs-method Maintain and use BAM files
readBamGappedAlignmentPairs-method Reading a BAM file into a GappedAlignments, GappedReads, or GappedAlignmentPairs object
readBamGappedAlignments Reading a BAM file into a GappedAlignments, GappedReads, or GappedAlignmentPairs object
readBamGappedAlignments-method Maintain and use BAM files
readBamGappedAlignments-method Views into a set of BAM files
readBamGappedAlignments-method Reading a BAM file into a GappedAlignments, GappedReads, or GappedAlignmentPairs object
readBamGappedReads Reading a BAM file into a GappedAlignments, GappedReads, or GappedAlignmentPairs object
readBamGappedReads-method Maintain and use BAM files
readBamGappedReads-method Reading a BAM file into a GappedAlignments, GappedReads, or GappedAlignmentPairs object
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
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 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.
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