API for rbamtools
Read and Write BAM (Binary Alignment) Files

Global functions
.onUnload	Source code
GenomePartition-class	Man page
[,bamRange,ANY,ANY,ANY-method	Man page
[,exonAlignDepth,ANY,ANY,ANY-method	Man page
[,exonLoessModel,ANY,ANY,ANY-method	Man page
[,geneAlignDepth,ANY,ANY,ANY-method	Man page
[,refSeqDict,ANY,ANY,ANY-method	Man page
[,sampleBamFiles,ANY,ANY,ANY-method	Man page
[-methods	Man page
[<-,refSeqDict-method	Man page
addReadGroup	Man page
addReadGroup,headerReadGroup-method	Man page
addReadGroup-methods	Man page
addSeq	Man page
addSeq,refSeqDict-method	Man page
aldRatio	Man page
aldRatio,exonAlignDepth-method	Man page
aldRatio-methods	Man page
alignDepth	Man page
alignDepth,bamRange-method	Man page
alignDepth-class	Man page
alignDepth-methods	Man page
alignQual	Man page
alignQual,bamAlign-method	Man page
alignQual-methods	Man page
alignQualVal	Man page
alignQualVal,bamAlign-method	Man page
alignQualVal-methods	Man page
alignSeq	Man page
alignSeq,bamAlign-method	Man page
alignSeq-methods	Man page
as.character	Man page
as.character,bamHeader-method	Man page
as.data.frame,refSeqDict-method	Man page
as.data.frame-methods	Man page
as.data.frame.bamGapList	Man page Source code
as.data.frame.bamRange	Man page Source code
as.data.frame.gapList	Man page Source code
as.data.frame.gapSiteList	Man page Source code
as.data.frame.rangeSegCount	Man page Source code
as.data.frame.refSeqDict	Man page Source code
as.list,headerLine-method	Man page
as.list,headerProgram-method	Man page
as.list,headerReadGroup-method	Man page
at_gc_ratio	Source code
bamAlign	Man page Source code
bamAlign-class	Man page
bamClose	Man page
bamClose,bamReader-method	Man page
bamClose,bamWriter-method	Man page
bamClose-methods	Man page
bamCopy	Man page
bamCopy,bamReader,bamWriter-method	Man page
bamCopy-methods	Man page
bamCount	Man page
bamCount,bamReader-method	Man page
bamCount-methods	Man page
bamCountAll	Man page
bamCountAll,bamReader,ANY-method	Man page
bamCountAll,sampleBamFiles,logical-method	Man page
bamCountAll,sampleBamFiles,missing-method	Man page
bamCountAll-methods	Man page
bamFiles	Man page
bamFiles,sampleBamFiles-method	Man page
bamFiles-methods	Man page
bamFiles<-	Man page
bamFiles<-,sampleBamFiles,character,logical-method	Man page
bamFiles<-,sampleBamFiles,character-method	Man page
bamFiles<--methods	Man page
bamGapList	Man page
bamGapList,bamReader-method	Man page
bamGapList-class	Man page
bamGapList-methods	Man page
bamHeader	Man page
bamHeader,bamHeaderText-method	Man page
bamHeader-class	Man page
bamHeaderText	Man page Source code
bamHeaderText-class	Man page
bamIdxFiles	Man page
bamIdxFiles,sampleBamFiles-method	Man page
bamIdxFiles-methods	Man page
bamIdxFiles<-	Man page
bamIdxFiles<-,sampleBamFiles,character-method	Man page
bamIdxFiles<--methods	Man page
bamRange	Man page Source code
bamRange-class	Man page
bamReader	Man page Source code
bamReader-class	Man page
bamSave	Man page
bamSave,bamReader,ANY,ANY-method	Man page
bamSave,bamReader,bamWriter,missing-method	Man page
bamSave,bamReader-method	Man page
bamSave,bamWriter,bamAlign,numeric-method	Man page
bamSave,bamWriter,bamRange,character-method	Man page
bamSave,bamWriter,bamRange,missing-method	Man page
bamSave,bamWriter,bamRange,numeric-method	Man page
bamSave,bamWriter-method	Man page
bamSave-methods	Man page
bamSort	Man page
bamSort,bamReader,ANY,ANY,ANY-method	Man page
bamSort,bamReader-method	Man page
bamSort,sampleBamFiles,ANY,ANY,ANY-method	Man page
bamSort,sampleBamFiles-method	Man page
bamSort-methods	Man page
bamWriter	Man page
bamWriter,bamHeader-method	Man page
bamWriter-class	Man page
checkBamFiles	Man page
checkBamFiles,sampleBamFiles-method	Man page
checkBamFiles-methods	Man page
checkPartition	Man page
checkPartition,GenomePartition,data.frame-method	Man page
checkPartition-methods	Man page
cigarData	Man page
cigarData,bamAlign-method	Man page
cigarData-methods	Man page
coerce, rangeSegCount, data.frame-method	Man page
coerce,bamGapList,data.frame-method	Man page
coerce,bamRange,data.frame-method	Man page
coerce,gapList,data.frame-method	Man page
coerce,gapSiteList,data.frame-method	Man page
coerce,refSeqDict,data.frame-method	Man page
copy_fastq	Source code
countNucs	Man page
countNucs,bamAlign-method	Man page
countNucs,bamRange-method	Man page
countNucs-methods	Man page
countPartition	Man page
countPartition,GenomePartition,bamReader-method	Man page
countPartition,GenomePartition,data.frame-method	Man page
countPartition-methods	Man page
countTextLines	Man page Source code
createIdxBatch	Man page Source code
createIndex	Man page
createIndex,bamReader,character-method	Man page
createIndex,bamReader,missing-method	Man page
createIndex,sampleBamFiles,character-method	Man page
createIndex,sampleBamFiles,missing-method	Man page
createIndex-methods	Man page
cutFlatAlignDepth	Man page
cutFlatAlignDepth,exonAlignDepth-method	Man page
cutFlatAlignDepth,exonLoessModel-method	Man page
cutFlatAlignDepth-methods	Man page
dim,refSeqDict-method	Man page
exonAlignDepth	Man page
exonAlignDepth,geneAlignDepth-method	Man page
exonAlignDepth-class	Man page
exonAlignDepth-methods	Man page
exonLoessModel	Man page
exonLoessModel,exonAlignDepth-method	Man page
exonLoessModel-class	Man page
exonLoessModel-methods	Man page
extractBamRegions	Man page Source code
extractGeneRegions	Man page
extractGeneRegions,bamReader,bamWriter,geneList-method	Man page
extractGeneRegions,bamReader,character,geneList-method	Man page
extractGeneRegions,sampleBamFiles,sampleBamFiles,geneList-method	Man page
extractGeneRegions-methods	Man page
extractRanges	Man page
extractRanges,bamReader-method	Man page
extractRanges-methods	Man page
failedQC	Man page
failedQC,bamAlign-method	Man page
failedQC-methods	Man page
failedQC<-	Man page
failedQC<-,bamAlign-method	Man page
failedQC<--methods	Man page
filename	Man page
filename,bamReader-method	Man page
filename,bamWriter-method	Man page
filename-methods	Man page
firstInPair	Man page
firstInPair,bamAlign-method	Man page
firstInPair-methods	Man page
firstInPair<-	Man page
firstInPair<-,bamAlign-method	Man page
firstInPair<--methods	Man page
flag	Man page
flag,bamAlign-method	Man page
flag-methods	Man page
flag<-	Man page
flag<-,bamAlign-method	Man page
flag<--methods	Man page
gapList	Man page
gapList,bamReader,numeric-method	Man page
gapList-class	Man page
gapSiteList-class	Man page
gc_content	Source code
geneAlignDepth	Man page
geneAlignDepth,sampleBamFiles,geneModel-method	Man page
geneAlignDepth-class	Man page
geneAlignDepth-methods	Man page
genomePartition	Man page
genomePartition,bamReader,data.frame-method	Man page
genomePartition-methods	Man page
getAlignCounts	Man page
getAlignCounts,GenomePartition-method	Man page
getAlignCounts-methods	Man page
getAlignRange	Man page
getAlignRange,bamRange-method	Man page
getAlignRange-methods	Man page
getCoords	Man page
getCoords,bamRange-method	Man page
getCoords-methods	Man page
getDepth	Man page
getDepth,alignDepth-method	Man page
getDepth-methods	Man page
getFileTable	Man page
getFileTable,GenomePartition-method	Man page
getFileTable-methods	Man page
getGridAlignCounts	Man page
getGridAlignCounts,GenomePartition-method	Man page
getGridAlignCounts-methods	Man page
getHeader	Man page
getHeader,bamHeaderText-method	Man page
getHeader,bamReader-method	Man page
getHeaderText	Man page
getHeaderText,bamHeader-method	Man page
getHeaderText,bamHeaderText-method	Man page
getHeaderText,bamReader-method	Man page
getHeaderText,headerLine-method	Man page
getHeaderText,headerProgram-method	Man page
getHeaderText,headerReadGroup-method	Man page
getHeaderText,refSeqDict-method	Man page
getHeaderText-methods	Man page
getNextAlign	Man page
getNextAlign,bamRange-method	Man page
getNextAlign,bamReader-method	Man page
getNextAlign-methods	Man page
getNormFactor	Man page
getNormFactor,exonAlignDepth-method	Man page
getNormFactor-methods	Man page
getParams	Man page
getParams,alignDepth-method	Man page
getParams,bamRange-method	Man page
getParams-methods	Man page
getPos	Man page
getPos,alignDepth-method	Man page
getPos-methods	Man page
getPrevAlign	Man page
getPrevAlign,bamRange-method	Man page
getPrevAlign-methods	Man page
getQualDf	Man page
getQualDf,bamRange,logical-method	Man page
getQualDf,bamRange,missing-method	Man page
getQualDf-methods	Man page
getQualQuantiles	Man page
getQualQuantiles,bamRange,numeric-method	Man page
getQualQuantiles-methods	Man page
getRefCoords	Man page
getRefCoords,bamReader,character-method	Man page
getRefCoords,bamReader,factor-method	Man page
getRefCoords-methods	Man page
getRefCount	Man page
getRefCount,bamReader-method	Man page
getRefCount-methods	Man page
getRefData	Man page
getRefData,GenomePartition-method	Man page
getRefData,bamReader-method	Man page
getRefData,bamWriter-method	Man page
getRefData-methods	Man page
getRefId	Man page
getRefId,bamReader,character-method	Man page
getRefId,bamReader,factor-method	Man page
getRefId,bamWriter,character-method	Man page
getRefId,bamWriter,factor-method	Man page
getRefId-methods	Man page
getRefName	Man page
getRefName,bamRange-method	Man page
getRefName-methods	Man page
getSeqLen	Man page
getSeqLen,bamRange-method	Man page
getSeqLen-methods	Man page
getSeqNr	Man page
getSeqNr,GenomePartition-method	Man page
getSeqNr-methods	Man page
getVal	Man page
getVal,headerLine-method	Man page
getVal,headerProgram-method	Man page
getVal,headerReadGroup-method	Man page
groupAldMatrix	Man page
groupAldMatrix,exonAlignDepth-method	Man page
groupAldMatrix-methods	Man page
groupAldTable	Man page
groupAldTable,exonAlignDepth-method	Man page
groupAldTable-methods	Man page
groupRatio	Man page
groupRatio,exonLoessModel-method	Man page
groupRatio-methods	Man page
groupTable	Man page
groupTable,sampleBamFiles-method	Man page
groupTable-methods	Man page
groupTable<-	Man page
groupTable<-,sampleBamFiles,character-method	Man page
groupTable<-,sampleBamFiles,data.frame-method	Man page
groupTable<--methods	Man page
head	Man page
head,refSeqDict-method	Man page
headerLine	Man page
headerLine,bamHeaderText-method	Man page
headerLine-class	Man page
headerLine<-	Man page
headerLine<-,bamHeaderText-method	Man page
headerProgram	Man page
headerProgram,bamHeaderText-method	Man page
headerProgram-class	Man page
headerProgram<-	Man page
headerProgram<-,bamHeaderText-method	Man page
headerReadGroup	Man page
headerReadGroup,bamHeaderText-method	Man page
headerReadGroup-class	Man page
headerReadGroup<-	Man page
headerReadGroup<-,bamHeaderText-method	Man page
indexInitialized	Man page
indexInitialized,bamReader-method	Man page
indexInitialized-methods	Man page
initialize, exonAlignDepth	Man page
initialize, exonLoessModel	Man page
initialize, geneAlignDepth	Man page
initialize, rangeSegCount-method	Man page
initialize, sampleBamFiles	Man page
initialize,bamAlign-method	Man page
initialize,bamGapList-method	Man page
initialize,bamHeader-method	Man page
initialize,bamHeaderText-method	Man page
initialize,bamRange-method	Man page
initialize,bamWriter-method	Man page
initialize,gapList-method	Man page
initialize,gapSiteList-method	Man page
initialize,headerLine-method	Man page
initialize,headerProgram-method	Man page
initialize,headerReadGroup-method	Man page
initialize,refSeqDict-method	Man page
insertPastCurrent	Man page
insertPastCurrent,bamRange-method	Man page
insertPastCurrent-methods	Man page
insertPreCurrent	Man page
insertPreCurrent,bamRange-method	Man page
insertPreCurrent-methods	Man page
insertSize	Man page
insertSize,bamAlign-method	Man page
insertSize-methods	Man page
isOpen	Man page
isOpen,bamReader-method	Man page
isOpen,bamWriter-method	Man page
isOpen-methods	Man page
junctionSites	Man page
junctionSites,exonAlignDepth-method	Man page
junctionSites-methods	Man page
length,exonAlignDepth-method	Man page
length,exonLoessModel-method	Man page
length,geneAlignDepth-method	Man page
length,sampleBamFiles-method	Man page
loadIndex	Man page
loadIndex,bamReader-method	Man page
loadIndex-methods	Man page
mapQuality	Man page
mapQuality,bamAlign-method	Man page
mapQuality-methods	Man page
matePosition	Man page
matePosition,bamAlign-method	Man page
matePosition-methods	Man page
mateRefID	Man page
mateRefID,bamAlign-method	Man page
mateRefID-methods	Man page
mateReverseStrand	Man page
mateReverseStrand,bamAlign-method	Man page
mateReverseStrand-methods	Man page
mateReverseStrand<-	Man page
mateReverseStrand<-,bamAlign-method	Man page
mateReverseStrand<--methods	Man page
mateUnmapped	Man page
mateUnmapped,bamAlign-method	Man page
mateUnmapped-methods	Man page
mateUnmapped<-	Man page
mateUnmapped<-,bamAlign-method	Man page
mateUnmapped<--methods	Man page
meltDownSegments	Man page
meltDownSegments,rangeSegCount-method	Man page
meltDownSegments-methods	Man page
merge.bamGapList	Man page Source code
merge.gapSiteList	Man page Source code
moveCurrentAlign	Man page
moveCurrentAlign,bamRange-method	Man page
moveCurrentAlign-methods	Man page
multSeq	Man page Source code
nAlignGaps	Man page
nAlignGaps,bamGapList-method	Man page
nAlignGaps,gapList-method	Man page
nAlignGaps,gapSiteList-method	Man page
nAlignGaps-methods	Man page
nAligns	Man page
nAligns,bamGapList-method	Man page
nAligns,gapList-method	Man page
nAligns,gapSiteList-method	Man page
nAligns,sampleBamFiles-method	Man page
nAligns-methods	Man page
nAligns<-	Man page
nAligns<-,sampleBamFiles,character,numeric-method	Man page
nAligns<-,sampleBamFiles,integer-method	Man page
nAligns<-,sampleBamFiles,numeric-method	Man page
nAligns<--methods	Man page
nCigar	Man page
nCigar,bamAlign-method	Man page
nCigar-methods	Man page
name	Man page
name,bamAlign-method	Man page
name-methods	Man page
nucStats	Man page
nucStats,bamRange-method	Man page
nucStats,bamReader-method	Man page
nucStats,character-method	Man page
nucStats-methods	Man page
paired	Man page
paired,bamAlign-method	Man page
paired-methods	Man page
paired<-	Man page
paired<-,bamAlign-method	Man page
paired<--methods	Man page
pcrORopt_duplicate	Man page
pcrORopt_duplicate,bamAlign-method	Man page
pcrORopt_duplicate-methods	Man page
pcrORopt_duplicate<-	Man page
pcrORopt_duplicate<-,bamAlign-method	Man page
pcrORopt_duplicate<--methods	Man page
plot.exonAlignDepth	Source code
plot.exonLoessModel	Source code
plot.geneAlignDepth	Source code
plotAlignDepth	Man page
plotAlignDepth,alignDepth-method	Man page
plotAlignDepth-methods	Man page
plotQualQuant	Man page
plotQualQuant,bamRange-method	Man page
plotQualQuant-methods	Man page
pop_back	Man page
pop_back,bamRange-method	Man page
pop_back-methods	Man page
pop_front	Man page
pop_front,bamRange-method	Man page
pop_front-methods	Man page
position	Man page
position,bamAlign-method	Man page
position-methods	Man page
properPair	Man page
properPair,bamAlign-method	Man page
properPair-methods	Man page
properPair<-	Man page
properPair<-,bamAlign-method	Man page
properPair<--methods	Man page
push_back	Man page
push_back,bamRange-method	Man page
push_back-methods	Man page
push_front	Man page
push_front,bamRange-method	Man page
push_front-methods	Man page
rangeSegCount	Man page Man page
rangeSegCount,bamReader-method	Man page
rangeSegCount-class	Man page
rangeSegCount-methods	Man page
rangeToFastq	Man page
rangeToFastq,bamRange,character-method	Man page
rangeToFastq-methods	Man page
rbamtools	Man page
rbamtools-package	Man page
readAccGapTables	Source code
readPooledBamGapDf	Man page Source code
readPooledBamGaps	Man page Source code
readRange	Man page
readRange,bamReader,character,numeric,logical-method	Man page
readRange,bamReader,character,numeric,missing-method	Man page
readRange,bamReader,factor,numeric,logical-method	Man page
readRange,bamReader,factor,numeric,missing-method	Man page
readRange-methods	Man page
readSepGapTables	Source code
readerToFastq	Man page
readerToFastq,bamReader-method	Man page
readerToFastq-methods	Man page
refID	Man page
refID,bamAlign-method	Man page
refID,gapSiteList-method	Man page
refID-methods	Man page
refID<-	Man page
refID<-,gapSiteList,numeric-method	Man page
refID<--methods	Man page
refSeqDict	Man page
refSeqDict,bamHeaderText-method	Man page
refSeqDict-class	Man page
refSeqDict<-	Man page
refSeqDict<-,bamHeaderText-method	Man page
removeSeqs	Man page
removeSeqs,refSeqDict-method	Man page
reverseStrand	Man page
reverseStrand,bamAlign-method	Man page
reverseStrand-methods	Man page
reverseStrand<-	Man page
reverseStrand<-,bamAlign-method	Man page
reverseStrand<--methods	Man page
rewind	Man page
rewind,bamRange-method	Man page
rewind,bamReader-method	Man page
rewind-methods	Man page
sampleBamFiles	Man page
sampleBamFiles,character-method	Man page
sampleBamFiles,factor-method	Man page
sampleBamFiles,integer-method	Man page
sampleBamFiles,numeric-method	Man page
sampleBamFiles-class	Man page
sampleBamFiles-methods	Man page
sampleGroups	Man page
sampleGroups,sampleBamFiles-method	Man page
sampleGroups-methods	Man page
sampleGroups<-	Man page
sampleGroups<-,sampleBamFiles,character-method	Man page
sampleGroups<-,sampleBamFiles,factor-method	Man page
sampleGroups<--methods	Man page
sampleLabels	Man page
sampleLabels,sampleBamFiles-method	Man page
sampleLabels-methods	Man page
sampleLabels<-	Man page
sampleLabels<-,sampleBamFiles,character-method	Man page
sampleLabels<-,sampleBamFiles,factor-method	Man page
sampleLabels<-,sampleBamFiles,integer-method	Man page
sampleLabels<--methods	Man page
saveAldData	Man page
saveAldData,sampleBamFiles,geneList-method	Man page
saveAldData-methods	Man page
secondInPair	Man page
secondInPair,bamAlign-method	Man page
secondInPair-methods	Man page
secondInPair<-	Man page
secondInPair<-,bamAlign-method	Man page
secondInPair<--methods	Man page
secondaryAlign	Man page
secondaryAlign,bamAlign-method	Man page
secondaryAlign-methods	Man page
secondaryAlign<-	Man page
secondaryAlign<-,bamAlign-method	Man page
secondaryAlign<--methods	Man page
segmentize	Man page
segmentize,ANY-method	Man page
segmentize,data.frame-method	Man page
segmentize,matrix-method	Man page
segmentize-methods	Man page
seqSegments	Source code
setVal	Man page
setVal,headerLine-method	Man page
setVal,headerProgram-method	Man page
setVal,headerReadGroup-method	Man page
show,GenomePartition-method	Man page
show,alignDepth-method	Man page
show,bamGapList-method	Man page
show,bamHeader-method	Man page
show,exonAlignDepth-method	Man page
show,exonLoessModel-method	Man page
show,gapList-method	Man page
show,gapSiteList-method	Man page
show,geneAlignDepth-method	Man page
show,sampleBamFiles-method	Man page
siteList	Man page
siteList,bamRange,missing-method	Man page
siteList,bamReader,numeric-method	Man page
siteList,missing,missing-method	Man page
siteList,numeric,missing-method	Man page
size	Man page
size,bamGapList-method	Man page
size,bamRange-method	Man page
size,gapList-method	Man page
size,gapSiteList-method	Man page
size,rangeSegCount-method	Man page
size-methods	Man page
stepNextAlign	Man page
stepNextAlign,bamRange-method	Man page
stepNextAlign-methods	Man page
stepPrevAlign	Man page
stepPrevAlign,bamRange-method	Man page
stepPrevAlign-methods	Man page
summary.bamGapList	Man page Source code
suppAlign	Man page
suppAlign,bamAlign-method	Man page
suppAlign-methods	Man page
suppAlign<-	Man page
suppAlign<-,bamAlign-method	Man page
suppAlign<--methods	Man page
tail	Man page
tail,refSeqDict-method	Man page
unmapped	Man page
unmapped,bamAlign-method	Man page
unmapped-methods	Man page
unmapped<-	Man page
unmapped<-,bamAlign-method	Man page
unmapped<--methods	Man page
writeCurrentAlign	Man page
writeCurrentAlign,bamRange-method	Man page
writeCurrentAlign-methods	Man page