Reading, manipulation and writing BAM (Binary alignment) files.

Documentation for package ‘rbamtools’ version 2.4.0

DESCRIPTION file.

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A B C D F G H I L M N P R S T U W misc

rbamtools-package

Reading, writing and manipulating BAM-file format.

-- A --

addSeq	Class '"refSeqDict"'
addSeq-method	Class '"refSeqDict"'
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"'

-- B --

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"'
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	Class '"bamReader"'
bamSort-method	Class '"bamReader"'
bamWriter	bamWriter Object
bamWriter-class	Class '"bamWriter"'
bamWriter-method	Class '"bamHeader"'

-- C --

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.index	Class '"bamReader"'
create.index-method	Class '"bamReader"'
create.index-methods	Class '"bamReader"'

-- D --

dim-method

Class '"refSeqDict"'

-- F --

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"'

-- G --

gapList	Class '"gapList"'
gapList-class	Class '"gapList"'
gapList-method	Class '"gapList"'
gapSiteList-class	Class '"gapSiteList"'
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
getPrevAlign	Class '"bamRange"'
getPrevAlign-method	Class '"bamRange"'
getPrevAlign-methods	Class '"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"'
getVal	getVal(object,members)
getVal-method	Class '"headerLine"'
getVal-method	Class '"headerProgram"'
getVal-method	Class '"headerReadGroup"'

-- H --

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"'

-- I --

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)

-- L --

load.index	Class '"bamReader"'
load.index-method	Class '"bamReader"'

-- M --

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"'

-- N --

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	Class '"gapList"'
nGapAligns-method	Class '"bamGapList"'
nGapAligns-method	Class '"gapList"'
nGapAligns-method	Class '"gapSiteList"'
nGapAligns-methods	Class '"gapList"'

-- P --

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"'
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"'

-- R --

rbamtools	Reading, writing and manipulating BAM-file format.
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 '"bamReader"'
rewind-methods	Class '"bamReader"'

-- S --

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 '"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"'

-- T --

tail	Class '"refSeqDict"'
tail-method	Class '"refSeqDict"'

-- U --

unmapped	Class '"bamAlign"'
unmapped-method	Class '"bamAlign"'
unmapped-methods	Class '"bamAlign"'
unmapped<-	Class '"bamAlign"'
unmapped<--method	Class '"bamAlign"'
unmapped<--methods	Class '"bamAlign"'

-- W --

windBack	Class '"bamRange"'
windBack-method	Class '"bamRange"'
windBack-methods	Class '"bamRange"'
writeCurrentAlign	Class '"bamRange"'
writeCurrentAlign-method	Class '"bamRange"'
writeCurrentAlign-methods	Class '"bamRange"'

-- misc --

[-method	Class '"refSeqDict"'
[<--method	Class '"refSeqDict"'