A B C D E F G H I L M N P R S T U W misc
rbamtools-package | Reading, writing and manipulating BAM-file format. |
addSeq | Class '"refSeqDict"' |
addSeq-method | Class '"refSeqDict"' |
alignDepth | Class '"alignDepth"' |
alignDepth-class | Class '"alignDepth"' |
alignDepth-method | Class '"alignDepth"' |
alignDepth-methods | Class '"alignDepth"' |
alignQual | Class '"bamAlign"' |
alignQual-method | Class '"bamAlign"' |
alignQual-methods | Class '"bamAlign"' |
alignSeq | Class '"bamAlign"' |
alignSeq-method | Class '"bamAlign"' |
alignSeq-methods | Class '"bamAlign"' |
as.character | Class '"bamHeader"' |
as.character-method | Class '"bamHeader"' |
as.data.frame-method | Class '"refSeqDict"' |
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"' |
as.data.frame.gapList | Class '"gapList"' |
as.data.frame.gapSiteList | Class '"gapSiteList"' |
as.data.frame.refSeqDict | Class '"refSeqDict"' |
as.list-method | Class '"headerLine"' |
as.list-method | Class '"headerProgram"' |
as.list-method | Class '"headerReadGroup"' |
bamAlign | bamAlign |
bamAlign-class | Class '"bamAlign"' |
bamClose | bamClose(bamReader), bamClose(bamWriter) |
bamClose-method | Class '"bamReader"' |
bamClose-method | Class '"bamWriter"' |
bamClose-methods | bamClose(bamReader), bamClose(bamWriter) |
bamCopy | Class '"bamReader"' |
bamCopy-method | Class '"bamReader"' |
bamCopy-methods | Class '"bamReader"' |
bamCount | bamCount |
bamCount-method | bamCount |
bamCount-methods | bamCount |
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"' |
bamHeader-class | Class '"bamHeader"' |
bamHeader-method | Class '"bamHeader"' |
bamHeaderText | Class '"bamHeader"' |
bamHeaderText-class | Class '"bamHeader"' |
bamRange | bamRange(bamReader, coordinates,complex=FALSE) |
bamRange-class | Class '"bamRange"' |
bamReader | bamReader |
bamReader-class | Class '"bamReader"' |
bamSave | Class '"bamWriter"' |
bamSave-method | Class '"bamReader"' |
bamSave-method | Class '"bamWriter"' |
bamSave-methods | Class '"bamWriter"' |
bamSort | bamSort |
bamSort-method | Class '"bamReader"' |
bamWriter | bamWriter Object |
bamWriter-class | Class '"bamWriter"' |
bamWriter-method | Class '"bamHeader"' |
cigarData | Class '"bamAlign"' |
cigarData-method | Class '"bamAlign"' |
cigarData-methods | Class '"bamAlign"' |
coerce-method | Class '"bamGapList"' |
coerce-method | Class '"bamRange"' |
coerce-method | Class '"gapList"' |
coerce-method | Class '"gapSiteList"' |
coerce-method | Class '"refSeqDict"' |
create.idx.batch | create.idx.batch |
create.index | Class '"bamReader"' |
create.index-method | Class '"bamReader"' |
create.index-methods | Class '"bamReader"' |
dim-method | Class '"refSeqDict"' |
extractRanges | extractRanges |
extractRanges-method | extractRanges |
extractRanges-methods | extractRanges |
failedQC | Class '"bamAlign"' |
failedQC-method | Class '"bamAlign"' |
failedQC-methods | Class '"bamAlign"' |
failedQC<- | Class '"bamAlign"' |
failedQC<--method | Class '"bamAlign"' |
failedQC<--methods | Class '"bamAlign"' |
filename | Reading 'filename' from bamReader or bamWriter |
filename-method | Class '"bamReader"' |
filename-method | Class '"bamWriter"' |
filename-methods | Reading 'filename' from bamReader or bamWriter |
firstInPair | Class '"bamAlign"' |
firstInPair-method | Class '"bamAlign"' |
firstInPair-methods | Class '"bamAlign"' |
firstInPair<- | Class '"bamAlign"' |
firstInPair<--method | Class '"bamAlign"' |
firstInPair<--methods | Class '"bamAlign"' |
flag | Class '"bamAlign"' |
flag-method | Class '"bamAlign"' |
flag-methods | Class '"bamAlign"' |
flag<- | Class '"bamAlign"' |
flag<--method | Class '"bamAlign"' |
flag<--methods | Class '"bamAlign"' |
gapList | Class '"gapList"' |
gapList-class | Class '"gapList"' |
gapList-method | Class '"gapList"' |
gapSiteList-class | Class '"gapSiteList"' |
getAlignRange | Class '"bamRange"' |
getAlignRange-method | Class '"bamRange"' |
getAlignRange-methods | Class '"bamRange"' |
getCoords | Class '"bamRange"' |
getCoords-method | Class '"bamRange"' |
getCoords-methods | Class '"bamRange"' |
getDepth | Class '"alignDepth"' |
getDepth-method | Class '"alignDepth"' |
getDepth-methods | Class '"alignDepth"' |
getHeader | Class '"bamHeader"' |
getHeader-method | Class '"bamHeader"' |
getHeader-method | Class '"bamReader"' |
getHeaderText | 'getHeaderText' Assembling member data into Header-Text |
getHeaderText-method | Class '"bamHeader"' |
getHeaderText-method | Class '"bamHeader"' |
getHeaderText-method | Class '"bamReader"' |
getHeaderText-method | Class '"headerLine"' |
getHeaderText-method | Class '"headerProgram"' |
getHeaderText-method | Class '"headerReadGroup"' |
getHeaderText-method | Class '"refSeqDict"' |
getHeaderText-methods | 'getHeaderText' Assembling member data into Header-Text |
getNextAlign | 'getNextAlign': Retrieving next align from bamReader or bamRange |
getNextAlign-method | Class '"bamRange"' |
getNextAlign-method | Class '"bamReader"' |
getNextAlign-methods | 'getNextAlign': Retrieving next align from bamReader or bamRange |
getParams | Class '"bamRange"' |
getParams-method | Class '"alignDepth"' |
getParams-method | Class '"bamRange"' |
getParams-methods | Class '"bamRange"' |
getPos | Class '"alignDepth"' |
getPos-method | Class '"alignDepth"' |
getPos-methods | Class '"alignDepth"' |
getPrevAlign | Class '"bamRange"' |
getPrevAlign-method | Class '"bamRange"' |
getPrevAlign-methods | Class '"bamRange"' |
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 | Class '"bamReader"' |
getRefCoords-method | Class '"bamReader"' |
getRefCoords-methods | Class '"bamReader"' |
getRefCount | Class '"bamReader"' |
getRefCount-method | Class '"bamReader"' |
getRefCount-methods | Class '"bamReader"' |
getRefData | Class '"bamReader"' |
getRefData-method | Class '"bamReader"' |
getRefData-methods | Class '"bamReader"' |
getRefName | Class '"bamRange"' |
getRefName-method | Class '"bamRange"' |
getRefName-methods | Class '"bamRange"' |
getSeqLen | Class '"bamRange"' |
getSeqLen-method | Class '"bamRange"' |
getSeqLen-methods | Class '"bamRange"' |
getVal | getVal(object,members) |
getVal-method | Class '"headerLine"' |
getVal-method | Class '"headerProgram"' |
getVal-method | Class '"headerReadGroup"' |
head | Class '"refSeqDict"' |
head-method | Class '"refSeqDict"' |
headerLine | Class '"bamHeader"' |
headerLine-class | Class '"headerLine"' |
headerLine-method | Class '"bamHeader"' |
headerLine<- | Class '"bamHeader"' |
headerLine<--method | Class '"bamHeader"' |
headerProgram | Class '"bamHeader"' |
headerProgram-class | Class '"headerProgram"' |
headerProgram-method | Class '"bamHeader"' |
headerProgram<- | Class '"bamHeader"' |
headerProgram<--method | Class '"bamHeader"' |
headerReadGroup | Class '"bamHeader"' |
headerReadGroup-class | Class '"headerReadGroup"' |
headerReadGroup-method | Class '"bamHeader"' |
headerReadGroup<- | Class '"bamHeader"' |
headerReadGroup<--method | Class '"bamHeader"' |
index.initialized | Class '"bamReader"' |
index.initialized-method | Class '"bamReader"' |
index.initialized-methods | Class '"bamReader"' |
initialize-method | Class '"bamAlign"' |
initialize-method | Class '"bamGapList"' |
initialize-method | Class '"bamHeader"' |
initialize-method | Class '"bamHeader"' |
initialize-method | Class '"bamRange"' |
initialize-method | Class '"bamReader"' |
initialize-method | Class '"bamWriter"' |
initialize-method | Class '"gapList"' |
initialize-method | Class '"gapSiteList"' |
initialize-method | Class '"headerLine"' |
initialize-method | Class '"headerProgram"' |
initialize-method | Class '"headerReadGroup"' |
initialize-method | Class '"refSeqDict"' |
insertPastCurrent | Class '"bamRange"' |
insertPastCurrent-method | Class '"bamRange"' |
insertPastCurrent-methods | Class '"bamRange"' |
insertPreCurrent | Class '"bamRange"' |
insertPreCurrent-method | Class '"bamRange"' |
insertPreCurrent-methods | Class '"bamRange"' |
insertSize | Class '"bamAlign"' |
insertSize-method | Class '"bamAlign"' |
insertSize-methods | Class '"bamAlign"' |
isOpen | isOpen(bamReader),isOpen(bamWriter) |
isOpen-method | Class '"bamReader"' |
isOpen-method | Class '"bamWriter"' |
isOpen-methods | isOpen(bamReader),isOpen(bamWriter) |
load.index | Class '"bamReader"' |
load.index-method | Class '"bamReader"' |
mapQuality | Class '"bamAlign"' |
mapQuality-method | Class '"bamAlign"' |
mapQuality-methods | Class '"bamAlign"' |
matePosition | Class '"bamAlign"' |
matePosition-method | Class '"bamAlign"' |
matePosition-methods | Class '"bamAlign"' |
mateRefID | Class '"bamAlign"' |
mateRefID-method | Class '"bamAlign"' |
mateRefID-methods | Class '"bamAlign"' |
mateReverseStrand | Class '"bamAlign"' |
mateReverseStrand-method | Class '"bamAlign"' |
mateReverseStrand-methods | Class '"bamAlign"' |
mateReverseStrand<- | Class '"bamAlign"' |
mateReverseStrand<--method | Class '"bamAlign"' |
mateReverseStrand<--methods | Class '"bamAlign"' |
mateUnmapped | Class '"bamAlign"' |
mateUnmapped-method | Class '"bamAlign"' |
mateUnmapped-methods | Class '"bamAlign"' |
mateUnmapped<- | Class '"bamAlign"' |
mateUnmapped<--method | Class '"bamAlign"' |
mateUnmapped<--methods | Class '"bamAlign"' |
merge.bamGapList | Class '"bamGapList"' |
merge.gapSiteList | Class '"gapSiteList"' |
moveCurrentAlign | Class '"bamRange"' |
moveCurrentAlign-method | Class '"bamRange"' |
moveCurrentAlign-methods | Class '"bamRange"' |
nAlignGaps | Class '"gapList"' |
nAlignGaps-method | Class '"bamGapList"' |
nAlignGaps-method | Class '"gapList"' |
nAlignGaps-method | Class '"gapSiteList"' |
nAlignGaps-methods | Class '"gapList"' |
nAligns | Class '"gapList"' |
nAligns-method | Class '"bamGapList"' |
nAligns-method | Class '"gapList"' |
nAligns-method | Class '"gapSiteList"' |
nAligns-methods | Class '"gapList"' |
name | Class '"bamAlign"' |
name-method | Class '"bamAlign"' |
name-methods | Class '"bamAlign"' |
nCigar | Class '"bamAlign"' |
nCigar-method | Class '"bamAlign"' |
nCigar-methods | Class '"bamAlign"' |
nGapAligns | nGapAligns |
nGapAligns-method | nGapAligns |
nGapAligns-methods | nGapAligns |
paired | Class '"bamAlign"' |
paired-method | Class '"bamAlign"' |
paired-methods | Class '"bamAlign"' |
paired<- | Class '"bamAlign"' |
paired<--method | Class '"bamAlign"' |
paired<--methods | Class '"bamAlign"' |
pcrORopt_duplicate | Class '"bamAlign"' |
pcrORopt_duplicate-method | Class '"bamAlign"' |
pcrORopt_duplicate-methods | Class '"bamAlign"' |
pcrORopt_duplicate<- | Class '"bamAlign"' |
pcrORopt_duplicate<--method | Class '"bamAlign"' |
pcrORopt_duplicate<--methods | Class '"bamAlign"' |
plotAlignDepth | Class '"alignDepth"' |
plotAlignDepth-method | Class '"alignDepth"' |
plotAlignDepth-methods | Class '"alignDepth"' |
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"' |
pop_back-method | Class '"bamRange"' |
pop_back-methods | Class '"bamRange"' |
pop_front | Class '"bamRange"' |
pop_front-method | Class '"bamRange"' |
pop_front-methods | Class '"bamRange"' |
position | Class '"bamAlign"' |
position-method | Class '"bamAlign"' |
position-methods | Class '"bamAlign"' |
properPair | Class '"bamAlign"' |
properPair-method | Class '"bamAlign"' |
properPair-methods | Class '"bamAlign"' |
properPair<- | Class '"bamAlign"' |
properPair<--method | Class '"bamAlign"' |
properPair<--methods | Class '"bamAlign"' |
push_back | Class '"bamRange"' |
push_back-method | Class '"bamRange"' |
push_back-methods | Class '"bamRange"' |
push_front | Class '"bamRange"' |
push_front-method | Class '"bamRange"' |
push_front-methods | Class '"bamRange"' |
range2fastq | range2fastq |
range2fastq-method | range2fastq |
range2fastq-methods | range2fastq |
rbamtools | Reading, writing and manipulating BAM-file format. |
reader2fastq | reader2fastq |
reader2fastq-method | reader2fastq |
reader2fastq-methods | reader2fastq |
readPooledBamGapDf | readPooledBamGapDf |
readPooledBamGaps | readPooledBamGaps |
refID | Class '"bamAlign"' |
refID-method | Class '"bamAlign"' |
refID-methods | Class '"bamAlign"' |
refSeqDict | Class '"bamHeader"' |
refSeqDict-class | Class '"refSeqDict"' |
refSeqDict-method | Class '"bamHeader"' |
refSeqDict<- | Class '"bamHeader"' |
refSeqDict<--method | Class '"bamHeader"' |
removeSeqs | Class '"refSeqDict"' |
removeSeqs-method | Class '"refSeqDict"' |
reverseStrand | Class '"bamAlign"' |
reverseStrand-method | Class '"bamAlign"' |
reverseStrand-methods | Class '"bamAlign"' |
reverseStrand<- | Class '"bamAlign"' |
reverseStrand<--method | Class '"bamAlign"' |
reverseStrand<--methods | Class '"bamAlign"' |
rewind | Class '"bamReader"' |
rewind-method | Class '"bamRange"' |
rewind-method | Class '"bamReader"' |
rewind-methods | Class '"bamReader"' |
secondaryAlign | Class '"bamAlign"' |
secondaryAlign-method | Class '"bamAlign"' |
secondaryAlign-methods | Class '"bamAlign"' |
secondaryAlign<- | Class '"bamAlign"' |
secondaryAlign<--method | Class '"bamAlign"' |
secondaryAlign<--methods | Class '"bamAlign"' |
secondInPair | Class '"bamAlign"' |
secondInPair-method | Class '"bamAlign"' |
secondInPair-methods | Class '"bamAlign"' |
secondInPair<- | Class '"bamAlign"' |
secondInPair<--method | Class '"bamAlign"' |
secondInPair<--methods | Class '"bamAlign"' |
setVal | setVal(object,members,values) |
setVal-method | Class '"headerLine"' |
setVal-method | Class '"headerProgram"' |
setVal-method | Class '"headerReadGroup"' |
show-method | Class '"alignDepth"' |
show-method | Class '"bamGapList"' |
show-method | Class '"gapList"' |
show-method | Class '"gapSiteList"' |
siteList | Class '"gapSiteList"' |
siteList-method | Class '"gapSiteList"' |
size | Class '"bamRange"' |
size-method | Class '"bamGapList"' |
size-method | Class '"bamRange"' |
size-method | Class '"gapList"' |
size-method | Class '"gapSiteList"' |
size-methods | Class '"bamRange"' |
stepNextAlign | Class '"bamRange"' |
stepNextAlign-method | Class '"bamRange"' |
stepNextAlign-methods | Class '"bamRange"' |
stepPrevAlign | Class '"bamRange"' |
stepPrevAlign-method | Class '"bamRange"' |
stepPrevAlign-methods | Class '"bamRange"' |
summary.bamGapList | Class '"bamGapList"' |
tail | Class '"refSeqDict"' |
tail-method | Class '"refSeqDict"' |
unmapped | Class '"bamAlign"' |
unmapped-method | Class '"bamAlign"' |
unmapped-methods | Class '"bamAlign"' |
unmapped<- | Class '"bamAlign"' |
unmapped<--method | Class '"bamAlign"' |
unmapped<--methods | Class '"bamAlign"' |
writeCurrentAlign | Class '"bamRange"' |
writeCurrentAlign-method | Class '"bamRange"' |
writeCurrentAlign-methods | Class '"bamRange"' |
[-method | Class '"refSeqDict"' |
[<--method | Class '"refSeqDict"' |