Global functions | |
---|---|
[,bamRange-method | Man page |
[,refSeqDict-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 |
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 |
as.data.frame.bamRange | Man page |
as.data.frame.gapList | Man page |
as.data.frame.gapSiteList | Man page |
as.data.frame.rangeSegCount | Man page |
as.data.frame.refSeqDict | Man page |
as.list,headerLine-method | Man page |
as.list,headerProgram-method | Man page |
as.list,headerReadGroup-method | Man page |
bamAlign | Man page |
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-method | Man page |
bamCopy-methods | Man page |
bamCount | Man page |
bamCount,bamReader-method | Man page |
bamCount-methods | Man page |
bamCountAll | Man page |
bamCountAll,bamReader-method | Man page |
bamCountAll-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 |
bamHeaderText-class | Man page |
bamRange | Man page |
bamRange-class | Man page |
bamReader | Man page |
bamReader-class | Man page |
bamSave | Man page |
bamSave,bamReader-method | Man page |
bamSave,bamWriter-method | Man page |
bamSave-methods | Man page |
bamSort | Man page |
bamSort,bamReader-method | Man page |
bamWriter | Man page |
bamWriter,bamHeader-method | Man page |
bamWriter-class | 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 |
countNucs | Man page |
countNucs,bamAlign-method | Man page |
countNucs,bamRange-method | Man page |
countNucs-methods | Man page |
countTextLines | Man page |
create.idx.batch | Man page |
create.index | Man page |
create.index,bamReader-method | Man page |
create.index-methods | Man page |
createIdxBatch | Man page |
createIndex | Man page |
createIndex,bamReader-method | Man page |
createIndex-methods | Man page |
dim,refSeqDict-method | Man page |
extractBamRegions | 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-method | Man page |
gapList-class | Man page |
gapSiteList-class | 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 |
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 |
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-method | Man page |
getQualDf-methods | Man page |
getQualQuantiles | Man page |
getQualQuantiles,bamRange-method | Man page |
getQualQuantiles-methods | Man page |
getRefCoords | Man page |
getRefCoords,bamReader-method | Man page |
getRefCoords-methods | Man page |
getRefCount | Man page |
getRefCount,bamReader-method | Man page |
getRefCount-methods | Man page |
getRefData | Man page |
getRefData,bamReader-method | Man page |
getRefData-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 |
getVal | Man page |
getVal,headerLine-method | Man page |
getVal,headerProgram-method | Man page |
getVal,headerReadGroup-method | 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 |
index.initialized | Man page |
index.initialized,bamReader-method | Man page |
index.initialized-methods | Man page |
indexInitialized | Man page |
indexInitialized,bamReader-method | Man page |
indexInitialized-methods | Man page |
initialize, rangeSegCount-method | 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,bamReader-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 |
load.index | Man page |
load.index,bamReader-method | Man page |
load.index-methods | 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 |
merge.gapSiteList | Man page |
moveCurrentAlign | Man page |
moveCurrentAlign,bamRange-method | Man page |
moveCurrentAlign-methods | Man page |
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-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 |
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 |
range2fastq | Man page |
range2fastq,bamRange-method | Man page |
range2fastq-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-method | Man page |
rangeToFastq-methods | Man page |
rbamtools | Man page |
rbamtools-package | Man page |
readPooledBamGapDf | Man page |
readPooledBamGaps | Man page |
reader2fastq | Man page |
reader2fastq,bamReader-method | Man page |
reader2fastq-methods | Man page |
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 |
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 |
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 |
setVal | Man page |
setVal,headerLine-method | Man page |
setVal,headerProgram-method | Man page |
setVal,headerReadGroup-method | Man page |
show,alignDepth-method | Man page |
show,bamGapList-method | Man page |
show,bamHeader-method | Man page |
show,gapList-method | Man page |
show,gapSiteList-method | Man page |
siteList | Man page |
siteList,bamReader-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-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 |
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 |
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