API for wokai/rbamtools
An R package for reading and writing BAM (Binary alignment) files.

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 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-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 Source code
bamHeaderText-class 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-method Man page
bamSave,bamWriter-method Man page
bamSave-methods Man page
bamSegments Source code
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
copy_fastq Source code
countNucs Man page
countNucs,bamAlign-method Man page
countNucs,bamRange-method Man page
countNucs-methods Man page
countTextLines Man page Source code
create.idx.batch Man page Source code
create.index Man page
create.index,bamReader-method Man page
create.index-methods Man page
createIdxBatch Man page Source code
createIndex Man page
createIndex,bamReader-method Man page
createIndex-methods Man page
dim,refSeqDict-method Man page
extractBamRegions Man page Source code
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
gc_content Source code
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 Source code
merge.gapSiteList Man page Source code
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
onUnload Source code
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
readAccGapTables Source code
readPooledBamGapDf Man page Source code
readPooledBamGaps Man page Source code
readSepGapTables Source code
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 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
wokai/rbamtools documentation built on May 28, 2017, 5:12 a.m.