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

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425
Source code
6
Man pages
43
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wokai/rbamtools: An R package for reading and writing BAM (Binary alignment) files.
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API

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
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
wokai/rbamtools documentation built on May 4, 2019, 9:46 a.m.

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