An R package for reading and writing BAM (Binary alignment) files.


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Documentation for package ‘rbamtools’ version 2.10.0

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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.
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.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-methods bamCountAll
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.
bamRange bamRange(bamReader, 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 Class '"bamWriter"': Representation of a file connection to a BAM file for writing access.
bamSave-method Class '"bamReader"': Representation for file connection to BAM file for reading access.
bamSave-method Class '"bamWriter"': Representation of a file connection to a BAM file for writing access.
bamSave-methods Class '"bamWriter"': Representation of a file connection to a BAM file for writing access.
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.
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 --

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 '"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'
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-methods Class '"bamReader"': Representation for file connection to BAM file for reading access.

-- D --

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

-- E --

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.
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.
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
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 Retrieve reference sequence from a BAM file as data.frame
getRefData-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.
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

-- 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-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 '"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.

-- L --

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.
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.

-- 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-methods Class '"gapList"': Representation of genomic alignment gaps.
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 range2fastq: Extract read information from alignments for given genomic range as fastq.
range2fastq-method range2fastq: Extract read information from alignments for given genomic range as fastq.
range2fastq-methods range2fastq: Extract read information from alignments for given genomic range as fastq.
rbamtools Reading, writing and manipulating BAM-file format.
reader2fastq reader2fastq: Extraction of a subset of alignments from a BAM files into fastq format.
reader2fastq-method reader2fastq: Extraction of a subset of alignments from a BAM files into fastq format.
reader2fastq-methods reader2fastq: 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.
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.
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 --

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.
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 '"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 '"gapList"': Representation of genomic alignment gaps.
show-method Class '"gapSiteList"': Representation of genomic alignment gap positions.
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-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 '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.
[-methods Class '"bamRange"': Representation of genomic alignments in defined regions.
[<--method Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header.