Read and Write BAM (Binary Alignment) Files

Documentation for package ‘rbamtools’ version 2.16.11

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A B C D E F G H I J L M N P R S T U W misc

Reading, writing and manipulating BAM-file format.

-- A --

addReadGroup	Class '"headerReadGroup"': Representation of read - group data in header section of BAM files
addReadGroup-method	Class '"headerReadGroup"': Representation of read - group data in header section of BAM files
addReadGroup-methods	Class '"headerReadGroup"': Representation of read - group data in header section of BAM files
addSeq	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.
addSeq-method	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.
aldRatio	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
aldRatio-method	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
aldRatio-methods	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
alignDepth	Class '"alignDepth"': Alignment depth information from bamRange objects.
alignDepth-class	Class '"alignDepth"': Alignment depth information from bamRange objects.
alignDepth-method	Class '"alignDepth"': Alignment depth information from bamRange objects.
alignDepth-methods	Class '"alignDepth"': Alignment depth information from bamRange objects.
alignQual	Class '"bamAlign"': Representation of single genomic alignments.
alignQual-method	Class '"bamAlign"': Representation of single genomic alignments.
alignQual-methods	Class '"bamAlign"': Representation of single genomic alignments.
alignQualVal	Class '"bamAlign"': Representation of single genomic alignments.
alignQualVal-method	Class '"bamAlign"': Representation of single genomic alignments.
alignQualVal-methods	Class '"bamAlign"': Representation of single genomic alignments.
alignSeq	Class '"bamAlign"': Representation of single genomic alignments.
alignSeq-method	Class '"bamAlign"': Representation of single genomic alignments.
alignSeq-methods	Class '"bamAlign"': Representation of single genomic alignments.
as.character	Class '"bamHeader"': Representation of data contained in the header section of BAM files.
as.character-method	Class '"bamHeader"': Representation of data contained in the header section of BAM files.
as.data.frame-method	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.
as.data.frame-methods	Conversion of bamRange or gapList into a data.frame
as.data.frame.bamGapList	Class '"bamGapList"'
as.data.frame.bamRange	Class '"bamRange"': Representation of genomic alignments in defined regions.
as.data.frame.gapList	Class '"gapList"': Representation of genomic alignment gaps.
as.data.frame.gapSiteList	Class '"gapSiteList"': Representation of genomic alignment gap positions.
as.data.frame.rangeSegCount	Class '"rangeSegCount"': Represents alignment counts in segments of genetic regions.
as.data.frame.refSeqDict	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.
as.list-method	Class '"headerLine"': Representation of header line segment of header section for BAM files.
as.list-method	Class '"headerProgram"': Represention of header - program section of BAM header.
as.list-method	Class '"headerReadGroup"': Representation of read - group data in header section of BAM files

-- B --

bamAlign	bamAlign
bamAlign-class	Class '"bamAlign"': Representation of single genomic alignments.
bamClose	bamClose(bamReader), bamClose(bamWriter): Closing of file connections.
bamClose-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
bamClose-method	Class '"bamWriter"': Representation of a file connection to a BAM file for writing access.
bamClose-methods	bamClose(bamReader), bamClose(bamWriter): Closing of file connections.
bamCopy	Class '"bamReader"': Representation for file connection to BAM file for reading access.
bamCopy-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
bamCopy-methods	Class '"bamReader"': Representation for file connection to BAM file for reading access.
bamCount	bamCount: Counting of CIGAR-OP items
bamCount-method	bamCount: Counting of CIGAR-OP items
bamCount-methods	bamCount: Counting of CIGAR-OP items
bamCountAll	bamCountAll
bamCountAll-method	bamCountAll
bamCountAll-method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
bamCountAll-methods	bamCountAll
bamFiles	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
bamFiles-method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
bamFiles-methods	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
bamFiles<-	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
bamFiles<--method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
bamFiles<--methods	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
bamGapList	Class '"bamGapList"'
bamGapList-class	Class '"bamGapList"'
bamGapList-method	Class '"bamGapList"'
bamGapList-methods	Class '"bamGapList"'
bamHeader	Class '"bamHeader"': Representation of data contained in the header section of BAM files.
bamHeader-class	Class '"bamHeader"': Representation of data contained in the header section of BAM files.
bamHeader-method	Class '"bamHeader"': Textual representation of header section of BAM files.
bamHeaderText	Class '"bamHeader"': Textual representation of header section of BAM files.
bamHeaderText-class	Class '"bamHeader"': Textual representation of header section of BAM files.
bamIdxFiles	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
bamIdxFiles-method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
bamIdxFiles-methods	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
bamIdxFiles<-	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
bamIdxFiles<--method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
bamIdxFiles<--methods	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
bamRange	bamRange(object, coordinates, complex=FALSE): Function for reading of alignments in genomic regions.
bamRange-class	Class '"bamRange"': Representation of genomic alignments in defined regions.
bamReader	bamReader: Connection to BAM file for reading access.
bamReader-class	Class '"bamReader"': Representation for file connection to BAM file for reading access.
bamSave	bamSave: Creation of a sorted copy of a BAM file.
bamSave-method	bamSave: Creation of a sorted copy of a BAM file.
bamSave-method	Class '"bamWriter"': Representation of a file connection to a BAM file for writing access.
bamSave-methods	bamSave: Creation of a sorted copy of a BAM file.
bamSort	bamSort: Creation of a sorted copy of a BAM file.
bamSort-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
bamSort-method	bamSort: Creation of a sorted copy of a BAM file.
bamSort-methods	bamSort: Creation of a sorted copy of a BAM file.
bamWriter	bamWriter: Opening a file connection to a BAM file for writing access.
bamWriter-class	Class '"bamWriter"': Representation of a file connection to a BAM file for writing access.
bamWriter-method	Class '"bamHeader"': Representation of data contained in the header section of BAM files.

-- C --

checkBamFiles	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
checkBamFiles-method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
checkBamFiles-methods	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
checkPartition	Class '"GenomePartition"': .
checkPartition-method	Class '"GenomePartition"': .
checkPartition-methods	Class '"GenomePartition"': .
cigarData	Class '"bamAlign"': Representation of single genomic alignments.
cigarData-method	Class '"bamAlign"': Representation of single genomic alignments.
cigarData-methods	Class '"bamAlign"': Representation of single genomic alignments.
coerce-method	Class '"bamGapList"'
coerce-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
coerce-method	Class '"gapList"': Representation of genomic alignment gaps.
coerce-method	Class '"gapSiteList"': Representation of genomic alignment gap positions.
coerce-method	Class '"rangeSegCount"': Represents alignment counts in segments of genetic regions.
coerce-method	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.
countNucs	Counting nucleotides in 'bamAlign' and 'bamRange'
countNucs-method	Counting nucleotides in 'bamAlign' and 'bamRange'
countNucs-methods	Counting nucleotides in 'bamAlign' and 'bamRange'
countPartition	Class '"GenomePartition"': .
countPartition-method	Class '"GenomePartition"': .
countPartition-methods	Class '"GenomePartition"': .
countTextLines	countTextLines: Counting lines in text files.
create.idx.batch	createIdxBatch: Creation of index files for multiple BAM files.
create.index	Class '"bamReader"': Representation for file connection to BAM file for reading access.
create.index-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
create.index-methods	Class '"bamReader"': Representation for file connection to BAM file for reading access.
createIdxBatch	createIdxBatch: Creation of index files for multiple BAM files.
createIndex	Class '"bamReader"': Representation for file connection to BAM file for reading access.
createIndex-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
createIndex-method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
createIndex-methods	Class '"bamReader"': Representation for file connection to BAM file for reading access.
cutFlatAlignDepth	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
cutFlatAlignDepth-method	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
cutFlatAlignDepth-method	Class '"exonLoessModel"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
cutFlatAlignDepth-methods	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.

-- D --

dim-method

Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.

-- E --

exonAlignDepth	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
exonAlignDepth-class	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
exonAlignDepth-method	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
exonAlignDepth-methods	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
exonLoessModel	Class '"exonLoessModel"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
exonLoessModel-class	Class '"exonLoessModel"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
exonLoessModel-method	Class '"exonLoessModel"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
exonLoessModel-methods	Class '"exonLoessModel"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
extractBamRegions	extractBamRegions: Extraction of alignments from given (genetic) regions and BAM files into a set of output BAM files..
extractGeneRegions	Extraction of alignments from given genetic regions and BAM files into a set of output BAM files.
extractGeneRegions-method	Extraction of alignments from given genetic regions and BAM files into a set of output BAM files.
extractGeneRegions-methods	Extraction of alignments from given genetic regions and BAM files into a set of output BAM files.
extractRanges	extractRanges: Extraction of alignments
extractRanges-method	extractRanges: Extraction of alignments
extractRanges-methods	extractRanges: Extraction of alignments

-- F --

failedQC	Class '"bamAlign"': Representation of single genomic alignments.
failedQC-method	Class '"bamAlign"': Representation of single genomic alignments.
failedQC-methods	Class '"bamAlign"': Representation of single genomic alignments.
failedQC<-	Class '"bamAlign"': Representation of single genomic alignments.
failedQC<--method	Class '"bamAlign"': Representation of single genomic alignments.
failedQC<--methods	Class '"bamAlign"': Representation of single genomic alignments.
filename	Reading 'filename' from bamReader or bamWriter
filename-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
filename-method	Class '"bamWriter"': Representation of a file connection to a BAM file for writing access.
filename-methods	Reading 'filename' from bamReader or bamWriter
firstInPair	Class '"bamAlign"': Representation of single genomic alignments.
firstInPair-method	Class '"bamAlign"': Representation of single genomic alignments.
firstInPair-methods	Class '"bamAlign"': Representation of single genomic alignments.
firstInPair<-	Class '"bamAlign"': Representation of single genomic alignments.
firstInPair<--method	Class '"bamAlign"': Representation of single genomic alignments.
firstInPair<--methods	Class '"bamAlign"': Representation of single genomic alignments.
flag	Class '"bamAlign"': Representation of single genomic alignments.
flag-method	Class '"bamAlign"': Representation of single genomic alignments.
flag-methods	Class '"bamAlign"': Representation of single genomic alignments.
flag<-	Class '"bamAlign"': Representation of single genomic alignments.
flag<--method	Class '"bamAlign"': Representation of single genomic alignments.
flag<--methods	Class '"bamAlign"': Representation of single genomic alignments.

-- G --

gapList	Class '"gapList"': Representation of genomic alignment gaps.
gapList-class	Class '"gapList"': Representation of genomic alignment gaps.
gapList-method	Class '"gapList"': Representation of genomic alignment gaps.
gapSiteList-class	Class '"gapSiteList"': Representation of genomic alignment gap positions.
geneAlignDepth	Class '"geneAlignDepth"': Align-depth data for single genes on multiple samples (BAM files).
geneAlignDepth-class	Class '"geneAlignDepth"': Align-depth data for single genes on multiple samples (BAM files).
geneAlignDepth-method	Class '"geneAlignDepth"': Align-depth data for single genes on multiple samples (BAM files).
geneAlignDepth-methods	Class '"geneAlignDepth"': Align-depth data for single genes on multiple samples (BAM files).
genomePartition	Class '"GenomePartition"': .
GenomePartition-class	Class '"GenomePartition"': .
genomePartition-method	Class '"GenomePartition"': .
genomePartition-methods	Class '"GenomePartition"': .
getAlignCounts	Class '"GenomePartition"': .
getAlignCounts-method	Class '"GenomePartition"': .
getAlignCounts-methods	Class '"GenomePartition"': .
getAlignRange	Class '"bamRange"': Representation of genomic alignments in defined regions.
getAlignRange-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
getAlignRange-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
getCoords	Class '"bamRange"': Representation of genomic alignments in defined regions.
getCoords-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
getCoords-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
getDepth	Class '"alignDepth"': Alignment depth information from bamRange objects.
getDepth-method	Class '"alignDepth"': Alignment depth information from bamRange objects.
getDepth-methods	Class '"alignDepth"': Alignment depth information from bamRange objects.
getFileTable	Class '"GenomePartition"': .
getFileTable-method	Class '"GenomePartition"': .
getFileTable-methods	Class '"GenomePartition"': .
getGridAlignCounts	Class '"GenomePartition"': .
getGridAlignCounts-method	Class '"GenomePartition"': .
getGridAlignCounts-methods	Class '"GenomePartition"': .
getHeader	Class '"bamHeader"': Textual representation of header section of BAM files.
getHeader-method	Class '"bamHeader"': Textual representation of header section of BAM files.
getHeader-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
getHeaderText	'getHeaderText' Assembling member data into Header-Text
getHeaderText-method	Class '"bamHeader"': Representation of data contained in the header section of BAM files.
getHeaderText-method	Class '"bamHeader"': Textual representation of header section of BAM files.
getHeaderText-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
getHeaderText-method	Class '"headerLine"': Representation of header line segment of header section for BAM files.
getHeaderText-method	Class '"headerProgram"': Represention of header - program section of BAM header.
getHeaderText-method	Class '"headerReadGroup"': Representation of read - group data in header section of BAM files
getHeaderText-method	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.
getHeaderText-methods	'getHeaderText' Assembling member data into Header-Text
getNextAlign	'getNextAlign': Retrieving next align from bamReader or bamRange
getNextAlign-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
getNextAlign-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
getNextAlign-methods	'getNextAlign': Retrieving next align from bamReader or bamRange
getNormFactor	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
getNormFactor-method	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
getNormFactor-methods	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
getParams	Class '"bamRange"': Representation of genomic alignments in defined regions.
getParams-method	Class '"alignDepth"': Alignment depth information from bamRange objects.
getParams-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
getParams-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
getPos	Class '"alignDepth"': Alignment depth information from bamRange objects.
getPos-method	Class '"alignDepth"': Alignment depth information from bamRange objects.
getPos-methods	Class '"alignDepth"': Alignment depth information from bamRange objects.
getPrevAlign	Class '"bamRange"': Representation of genomic alignments in defined regions.
getPrevAlign-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
getPrevAlign-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
getQualDf	Read and display Phred qualities from bamRange
getQualDf-method	Read and display Phred qualities from bamRange
getQualDf-methods	Read and display Phred qualities from bamRange
getQualQuantiles	Read and display Phred qualities from bamRange
getQualQuantiles-method	Read and display Phred qualities from bamRange
getQualQuantiles-methods	Read and display Phred qualities from bamRange
getRefCoords	Retrieve reference sequence from a BAM file as data.frame
getRefCoords-method	Retrieve reference sequence from a BAM file as data.frame
getRefCoords-methods	Retrieve reference sequence from a BAM file as data.frame
getRefCount	Retrieve reference sequence from a BAM file as data.frame
getRefCount-method	Retrieve reference sequence from a BAM file as data.frame
getRefCount-methods	Retrieve reference sequence from a BAM file as data.frame
getRefData	Retrieve reference sequence from a BAM file as data.frame
getRefData-method	Class '"GenomePartition"': .
getRefData-method	Retrieve reference sequence from a BAM file as data.frame
getRefData-methods	Retrieve reference sequence from a BAM file as data.frame
getRefId	Retrieve reference sequence from a BAM file as data.frame
getRefId-method	Retrieve reference sequence from a BAM file as data.frame
getRefId-methods	Retrieve reference sequence from a BAM file as data.frame
getRefName	Class '"bamRange"': Representation of genomic alignments in defined regions.
getRefName-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
getRefName-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
getSeqLen	Class '"bamRange"': Representation of genomic alignments in defined regions.
getSeqLen-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
getSeqLen-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
getSeqNr	Class '"GenomePartition"': .
getSeqNr-method	Class '"GenomePartition"': .
getSeqNr-methods	Class '"GenomePartition"': .
getVal	getVal(object,members): Retrieving values for given types from an object
getVal-method	Class '"headerLine"': Representation of header line segment of header section for BAM files.
getVal-method	Class '"headerProgram"': Represention of header - program section of BAM header.
getVal-method	Class '"headerReadGroup"': Representation of read - group data in header section of BAM files
groupAldMatrix	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
groupAldMatrix-method	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
groupAldMatrix-methods	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
groupAldTable	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
groupAldTable-method	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
groupAldTable-methods	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
groupRatio	Calculates group-wise ratios of alignment depth (AD)
groupRatio-method	Calculates group-wise ratios of alignment depth (AD)
groupRatio-methods	Calculates group-wise ratios of alignment depth (AD)
groupTable	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
groupTable-method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
groupTable-methods	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
groupTable<-	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
groupTable<--method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
groupTable<--methods	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.

-- H --

head	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.
head-method	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.
headerLine	Class '"bamHeader"': Textual representation of header section of BAM files.
headerLine-class	Class '"headerLine"': Representation of header line segment of header section for BAM files.
headerLine-method	Class '"bamHeader"': Textual representation of header section of BAM files.
headerLine<-	Class '"bamHeader"': Textual representation of header section of BAM files.
headerLine<--method	Class '"bamHeader"': Textual representation of header section of BAM files.
headerProgram	Class '"bamHeader"': Textual representation of header section of BAM files.
headerProgram-class	Class '"headerProgram"': Represention of header - program section of BAM header.
headerProgram-method	Class '"bamHeader"': Textual representation of header section of BAM files.
headerProgram<-	Class '"bamHeader"': Textual representation of header section of BAM files.
headerProgram<--method	Class '"bamHeader"': Textual representation of header section of BAM files.
headerReadGroup	Class '"bamHeader"': Textual representation of header section of BAM files.
headerReadGroup-class	Class '"headerReadGroup"': Representation of read - group data in header section of BAM files
headerReadGroup-method	Class '"bamHeader"': Textual representation of header section of BAM files.
headerReadGroup<-	Class '"bamHeader"': Textual representation of header section of BAM files.
headerReadGroup<--method	Class '"bamHeader"': Textual representation of header section of BAM files.

-- I --

index.initialized	Class '"bamReader"': Representation for file connection to BAM file for reading access.
index.initialized-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
index.initialized-methods	Class '"bamReader"': Representation for file connection to BAM file for reading access.
indexInitialized	Class '"bamReader"': Representation for file connection to BAM file for reading access.
indexInitialized-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
indexInitialized-methods	Class '"bamReader"': Representation for file connection to BAM file for reading access.
initialize, exonAlignDepth	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
initialize, exonLoessModel	Class '"exonLoessModel"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
initialize, geneAlignDepth	Class '"geneAlignDepth"': Align-depth data for single genes on multiple samples (BAM files).
initialize, sampleBamFiles	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
initialize-method	Class '"bamAlign"': Representation of single genomic alignments.
initialize-method	Class '"bamGapList"'
initialize-method	Class '"bamHeader"': Representation of data contained in the header section of BAM files.
initialize-method	Class '"bamHeader"': Textual representation of header section of BAM files.
initialize-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
initialize-method	Class '"bamWriter"': Representation of a file connection to a BAM file for writing access.
initialize-method	Class '"gapList"': Representation of genomic alignment gaps.
initialize-method	Class '"gapSiteList"': Representation of genomic alignment gap positions.
initialize-method	Class '"headerLine"': Representation of header line segment of header section for BAM files.
initialize-method	Class '"headerProgram"': Represention of header - program section of BAM header.
initialize-method	Class '"headerReadGroup"': Representation of read - group data in header section of BAM files
initialize-method	Class '"rangeSegCount"': Represents alignment counts in segments of genetic regions.
initialize-method	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.
insertPastCurrent	Class '"bamRange"': Representation of genomic alignments in defined regions.
insertPastCurrent-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
insertPastCurrent-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
insertPreCurrent	Class '"bamRange"': Representation of genomic alignments in defined regions.
insertPreCurrent-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
insertPreCurrent-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
insertSize	Class '"bamAlign"': Representation of single genomic alignments.
insertSize-method	Class '"bamAlign"': Representation of single genomic alignments.
insertSize-methods	Class '"bamAlign"': Representation of single genomic alignments.
isOpen	isOpen(bamReader), isOpen(bamWriter): Checking for opened file connection to BAM file.
isOpen-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
isOpen-method	Class '"bamWriter"': Representation of a file connection to a BAM file for writing access.
isOpen-methods	isOpen(bamReader), isOpen(bamWriter): Checking for opened file connection to BAM file.

-- J --

junctionSites	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
junctionSites-method	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
junctionSites-methods	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.

-- L --

length-method	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
length-method	Class '"exonLoessModel"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
length-method	Class '"geneAlignDepth"': Align-depth data for single genes on multiple samples (BAM files).
length-method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
load.index	Class '"bamReader"': Representation for file connection to BAM file for reading access.
load.index-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
load.index-methods	Class '"bamReader"': Representation for file connection to BAM file for reading access.
loadIndex	Class '"bamReader"': Representation for file connection to BAM file for reading access.
loadIndex-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
loadIndex-methods	Class '"bamReader"': Representation for file connection to BAM file for reading access.

-- M --

mapQuality	Class '"bamAlign"': Representation of single genomic alignments.
mapQuality-method	Class '"bamAlign"': Representation of single genomic alignments.
mapQuality-methods	Class '"bamAlign"': Representation of single genomic alignments.
matePosition	Class '"bamAlign"': Representation of single genomic alignments.
matePosition-method	Class '"bamAlign"': Representation of single genomic alignments.
matePosition-methods	Class '"bamAlign"': Representation of single genomic alignments.
mateRefID	Class '"bamAlign"': Representation of single genomic alignments.
mateRefID-method	Class '"bamAlign"': Representation of single genomic alignments.
mateRefID-methods	Class '"bamAlign"': Representation of single genomic alignments.
mateReverseStrand	Class '"bamAlign"': Representation of single genomic alignments.
mateReverseStrand-method	Class '"bamAlign"': Representation of single genomic alignments.
mateReverseStrand-methods	Class '"bamAlign"': Representation of single genomic alignments.
mateReverseStrand<-	Class '"bamAlign"': Representation of single genomic alignments.
mateReverseStrand<--method	Class '"bamAlign"': Representation of single genomic alignments.
mateReverseStrand<--methods	Class '"bamAlign"': Representation of single genomic alignments.
mateUnmapped	Class '"bamAlign"': Representation of single genomic alignments.
mateUnmapped-method	Class '"bamAlign"': Representation of single genomic alignments.
mateUnmapped-methods	Class '"bamAlign"': Representation of single genomic alignments.
mateUnmapped<-	Class '"bamAlign"': Representation of single genomic alignments.
mateUnmapped<--method	Class '"bamAlign"': Representation of single genomic alignments.
mateUnmapped<--methods	Class '"bamAlign"': Representation of single genomic alignments.
meltDownSegments	Class '"rangeSegCount"': Represents alignment counts in segments of genetic regions.
meltDownSegments-method	Class '"rangeSegCount"': Represents alignment counts in segments of genetic regions.
meltDownSegments-methods	Class '"rangeSegCount"': Represents alignment counts in segments of genetic regions.
merge.bamGapList	Class '"bamGapList"'
merge.gapSiteList	Class '"gapSiteList"': Representation of genomic alignment gap positions.
moveCurrentAlign	Class '"bamRange"': Representation of genomic alignments in defined regions.
moveCurrentAlign-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
moveCurrentAlign-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
multSeq	Create combined sequences of sequential numbers.

-- N --

nAlignGaps	Class '"gapList"': Representation of genomic alignment gaps.
nAlignGaps-method	Class '"bamGapList"'
nAlignGaps-method	Class '"gapList"': Representation of genomic alignment gaps.
nAlignGaps-method	Class '"gapSiteList"': Representation of genomic alignment gap positions.
nAlignGaps-methods	Class '"gapList"': Representation of genomic alignment gaps.
nAligns	Class '"gapList"': Representation of genomic alignment gaps.
nAligns-method	Class '"bamGapList"'
nAligns-method	Class '"gapList"': Representation of genomic alignment gaps.
nAligns-method	Class '"gapSiteList"': Representation of genomic alignment gap positions.
nAligns-method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
nAligns-methods	Class '"gapList"': Representation of genomic alignment gaps.
nAligns<-	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
nAligns<--method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
nAligns<--methods	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
name	Class '"bamAlign"': Representation of single genomic alignments.
name-method	Class '"bamAlign"': Representation of single genomic alignments.
name-methods	Class '"bamAlign"': Representation of single genomic alignments.
nCigar	Class '"bamAlign"': Representation of single genomic alignments.
nCigar-method	Class '"bamAlign"': Representation of single genomic alignments.
nCigar-methods	Class '"bamAlign"': Representation of single genomic alignments.
nucStats	Table nucleotides in whole BAM file(s)
nucStats-method	Table nucleotides in whole BAM file(s)
nucStats-methods	Table nucleotides in whole BAM file(s)

-- P --

paired	Class '"bamAlign"': Representation of single genomic alignments.
paired-method	Class '"bamAlign"': Representation of single genomic alignments.
paired-methods	Class '"bamAlign"': Representation of single genomic alignments.
paired<-	Class '"bamAlign"': Representation of single genomic alignments.
paired<--method	Class '"bamAlign"': Representation of single genomic alignments.
paired<--methods	Class '"bamAlign"': Representation of single genomic alignments.
pcrORopt_duplicate	Class '"bamAlign"': Representation of single genomic alignments.
pcrORopt_duplicate-method	Class '"bamAlign"': Representation of single genomic alignments.
pcrORopt_duplicate-methods	Class '"bamAlign"': Representation of single genomic alignments.
pcrORopt_duplicate<-	Class '"bamAlign"': Representation of single genomic alignments.
pcrORopt_duplicate<--method	Class '"bamAlign"': Representation of single genomic alignments.
pcrORopt_duplicate<--methods	Class '"bamAlign"': Representation of single genomic alignments.
plotAlignDepth	Class '"alignDepth"': Alignment depth information from bamRange objects.
plotAlignDepth-method	Class '"alignDepth"': Alignment depth information from bamRange objects.
plotAlignDepth-methods	Class '"alignDepth"': Alignment depth information from bamRange objects.
plotQualQuant	Read and display Phred qualities from bamRange
plotQualQuant-method	Read and display Phred qualities from bamRange
plotQualQuant-methods	Read and display Phred qualities from bamRange
pop_back	Class '"bamRange"': Representation of genomic alignments in defined regions.
pop_back-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
pop_back-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
pop_front	Class '"bamRange"': Representation of genomic alignments in defined regions.
pop_front-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
pop_front-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
position	Class '"bamAlign"': Representation of single genomic alignments.
position-method	Class '"bamAlign"': Representation of single genomic alignments.
position-methods	Class '"bamAlign"': Representation of single genomic alignments.
properPair	Class '"bamAlign"': Representation of single genomic alignments.
properPair-method	Class '"bamAlign"': Representation of single genomic alignments.
properPair-methods	Class '"bamAlign"': Representation of single genomic alignments.
properPair<-	Class '"bamAlign"': Representation of single genomic alignments.
properPair<--method	Class '"bamAlign"': Representation of single genomic alignments.
properPair<--methods	Class '"bamAlign"': Representation of single genomic alignments.
push_back	Class '"bamRange"': Representation of genomic alignments in defined regions.
push_back-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
push_back-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
push_front	Class '"bamRange"': Representation of genomic alignments in defined regions.
push_front-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
push_front-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.

-- R --

range2fastq	rangeToFastq: Extract read information from alignments for given genomic range as fastq.
range2fastq-method	rangeToFastq: Extract read information from alignments for given genomic range as fastq.
range2fastq-methods	rangeToFastq: Extract read information from alignments for given genomic range as fastq.
rangeSegCount	Class '"rangeSegCount"': Represents alignment counts in segments of genetic regions.
rangeSegCount-class	Class '"rangeSegCount"': Represents alignment counts in segments of genetic regions.
rangeSegCount-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
rangeSegCount-methods	Class '"bamReader"': Representation for file connection to BAM file for reading access.
rangeToFastq	rangeToFastq: Extract read information from alignments for given genomic range as fastq.
rangeToFastq-method	rangeToFastq: Extract read information from alignments for given genomic range as fastq.
rangeToFastq-methods	rangeToFastq: Extract read information from alignments for given genomic range as fastq.
rbamtools	Reading, writing and manipulating BAM-file format.
reader2fastq	readerToFastq: Extraction of a subset of alignments from a BAM files into fastq format.
reader2fastq-method	readerToFastq: Extraction of a subset of alignments from a BAM files into fastq format.
reader2fastq-methods	readerToFastq: Extraction of a subset of alignments from a BAM files into fastq format.
readerToFastq	readerToFastq: Extraction of a subset of alignments from a BAM files into fastq format.
readerToFastq-method	readerToFastq: Extraction of a subset of alignments from a BAM files into fastq format.
readerToFastq-methods	readerToFastq: Extraction of a subset of alignments from a BAM files into fastq format.
readPooledBamGapDf	readPooledBamGapDf: Position data for alignments gaps from multiple BAM files.
readPooledBamGaps	readPooledBamGaps: Position data for alignments gaps from multiple BAM files.
readRange	Class '"bamRange"': Representation of genomic alignments in defined regions.
readRange-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
readRange-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
refID	Class '"bamAlign"': Representation of single genomic alignments.
refID-method	Class '"bamAlign"': Representation of single genomic alignments.
refID-method	Class '"gapSiteList"': Representation of genomic alignment gap positions.
refID-methods	Class '"bamAlign"': Representation of single genomic alignments.
refID<-	Class '"gapSiteList"': Representation of genomic alignment gap positions.
refID<--method	Class '"gapSiteList"': Representation of genomic alignment gap positions.
refID<--methods	Class '"gapSiteList"': Representation of genomic alignment gap positions.
refSeqDict	Class '"bamHeader"': Textual representation of header section of BAM files.
refSeqDict-class	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.
refSeqDict-method	Class '"bamHeader"': Textual representation of header section of BAM files.
refSeqDict<-	Class '"bamHeader"': Textual representation of header section of BAM files.
refSeqDict<--method	Class '"bamHeader"': Textual representation of header section of BAM files.
removeSeqs	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.
removeSeqs-method	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.
reverseStrand	Class '"bamAlign"': Representation of single genomic alignments.
reverseStrand-method	Class '"bamAlign"': Representation of single genomic alignments.
reverseStrand-methods	Class '"bamAlign"': Representation of single genomic alignments.
reverseStrand<-	Class '"bamAlign"': Representation of single genomic alignments.
reverseStrand<--method	Class '"bamAlign"': Representation of single genomic alignments.
reverseStrand<--methods	Class '"bamAlign"': Representation of single genomic alignments.
rewind	Class '"bamReader"': Representation for file connection to BAM file for reading access.
rewind-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
rewind-method	Class '"bamReader"': Representation for file connection to BAM file for reading access.
rewind-methods	Class '"bamReader"': Representation for file connection to BAM file for reading access.

-- S --

sampleBamFiles	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
sampleBamFiles-class	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
sampleBamFiles-method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
sampleBamFiles-methods	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
sampleGroups	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
sampleGroups-method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
sampleGroups-methods	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
sampleGroups<-	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
sampleGroups<--method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
sampleGroups<--methods	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
sampleLabels	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
sampleLabels-method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
sampleLabels-methods	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
sampleLabels<-	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
sampleLabels<--method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
sampleLabels<--methods	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
saveAldData	saveAldData: Save alignment depth plots for single genes
saveAldData-method	saveAldData: Save alignment depth plots for single genes
saveAldData-methods	saveAldData: Save alignment depth plots for single genes
secondaryAlign	Class '"bamAlign"': Representation of single genomic alignments.
secondaryAlign-method	Class '"bamAlign"': Representation of single genomic alignments.
secondaryAlign-methods	Class '"bamAlign"': Representation of single genomic alignments.
secondaryAlign<-	Class '"bamAlign"': Representation of single genomic alignments.
secondaryAlign<--method	Class '"bamAlign"': Representation of single genomic alignments.
secondaryAlign<--methods	Class '"bamAlign"': Representation of single genomic alignments.
secondInPair	Class '"bamAlign"': Representation of single genomic alignments.
secondInPair-method	Class '"bamAlign"': Representation of single genomic alignments.
secondInPair-methods	Class '"bamAlign"': Representation of single genomic alignments.
secondInPair<-	Class '"bamAlign"': Representation of single genomic alignments.
secondInPair<--method	Class '"bamAlign"': Representation of single genomic alignments.
secondInPair<--methods	Class '"bamAlign"': Representation of single genomic alignments.
segmentize	Segmentation of vector using segment coordinates
segmentize-method	Segmentation of vector using segment coordinates
segmentize-methods	Segmentation of vector using segment coordinates
setVal	setVal(object,members,values): Setting values for given data items
setVal-method	Class '"headerLine"': Representation of header line segment of header section for BAM files.
setVal-method	Class '"headerProgram"': Represention of header - program section of BAM header.
setVal-method	Class '"headerReadGroup"': Representation of read - group data in header section of BAM files
show-method	Class '"GenomePartition"': .
show-method	Class '"alignDepth"': Alignment depth information from bamRange objects.
show-method	Class '"bamGapList"'
show-method	Class '"bamHeader"': Representation of data contained in the header section of BAM files.
show-method	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
show-method	Class '"exonLoessModel"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
show-method	Class '"gapList"': Representation of genomic alignment gaps.
show-method	Class '"gapSiteList"': Representation of genomic alignment gap positions.
show-method	Class '"geneAlignDepth"': Align-depth data for single genes on multiple samples (BAM files).
show-method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
siteList	Class '"gapSiteList"': Representation of genomic alignment gap positions.
siteList-method	Class '"gapSiteList"': Representation of genomic alignment gap positions.
size	Class '"bamRange"': Representation of genomic alignments in defined regions.
size-method	Class '"bamGapList"'
size-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
size-method	Class '"gapList"': Representation of genomic alignment gaps.
size-method	Class '"gapSiteList"': Representation of genomic alignment gap positions.
size-method	Class '"rangeSegCount"': Represents alignment counts in segments of genetic regions.
size-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
stepNextAlign	Class '"bamRange"': Representation of genomic alignments in defined regions.
stepNextAlign-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
stepNextAlign-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
stepPrevAlign	Class '"bamRange"': Representation of genomic alignments in defined regions.
stepPrevAlign-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
stepPrevAlign-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
summary.bamGapList	Class '"bamGapList"'
suppAlign	Class '"bamAlign"': Representation of single genomic alignments.
suppAlign-method	Class '"bamAlign"': Representation of single genomic alignments.
suppAlign-methods	Class '"bamAlign"': Representation of single genomic alignments.
suppAlign<-	Class '"bamAlign"': Representation of single genomic alignments.
suppAlign<--method	Class '"bamAlign"': Representation of single genomic alignments.
suppAlign<--methods	Class '"bamAlign"': Representation of single genomic alignments.

-- T --

tail	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.
tail-method	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.

-- U --

unmapped	Class '"bamAlign"': Representation of single genomic alignments.
unmapped-method	Class '"bamAlign"': Representation of single genomic alignments.
unmapped-methods	Class '"bamAlign"': Representation of single genomic alignments.
unmapped<-	Class '"bamAlign"': Representation of single genomic alignments.
unmapped<--method	Class '"bamAlign"': Representation of single genomic alignments.
unmapped<--methods	Class '"bamAlign"': Representation of single genomic alignments.

-- W --

writeCurrentAlign	Class '"bamRange"': Representation of genomic alignments in defined regions.
writeCurrentAlign-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
writeCurrentAlign-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.

-- misc --

[-method	Class '"bamRange"': Representation of genomic alignments in defined regions.
[-method	Class '"exonAlignDepth"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
[-method	Class '"exonLoessModel"': Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.
[-method	Class '"geneAlignDepth"': Align-depth data for single genes on multiple samples (BAM files).
[-method	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.
[-method	Class '"sampleBamFiles"': Data on multiple BAM files from an experimental setting.
[-methods	Class '"bamRange"': Representation of genomic alignments in defined regions.
[<--method	Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.