R: Read and Write BAM (Binary Alignment) Files

# Read and Write BAM (Binary Alignment) Files

## Documentation for package ‘rbamtools’ version 2.16.17

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

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

rbamtools-package | 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.
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 --

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.
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 --

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.
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.