rbamtools: Read and Write BAM (Binary Alignment) Files

Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.

AuthorWolfgang Kaisers
Date of publication2017-03-24 12:27:20 UTC
MaintainerWolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
LicenseArtistic-2.0
Version2.16.6

View on CRAN

Man pages

alignDepth-class: Class '"alignDepth"': Alignment depth information from...

as.data.frame-methods: Conversion of bamRange or gapList into a data.frame

bamAlign: bamAlign

bamAlign-class: Class '"bamAlign"': Representation of single genomic...

bamClose-methods: bamClose(bamReader), bamClose(bamWriter): Closing of file...

bamCount: bamCount: Counting of CIGAR-OP items

bamCountAll: bamCountAll

bamGapList-class: Class '"bamGapList"'

bamHeader-class: Class '"bamHeader"': Representation of data contained in the...

bamHeaderText-class: Class '"bamHeader"': Textual representation of header section...

bamRange: bamRange(object, coordinates, complex=FALSE): Function for...

bamRange-class: Class '"bamRange"': Representation of genomic alignments in...

bamReader: bamReader: Connection to BAM file for reading access.

bamReader-class: Class '"bamReader"': Representation for file connection to...

bamSave: bamSave: Creation of a sorted copy of a BAM file.

bamSort: bamSort: Creation of a sorted copy of a BAM file.

bamWriter: bamWriter: Opening a file connection to a BAM file for...

bamWriter-class: Class '"bamWriter"': Representation of a file connection to a...

countNucs: Counting nucleotides in 'bamAlign' and 'bamRange'

countTextLines: countTextLines: Counting lines in text files.

createIdxBatch: createIdxBatch: Creation of index files for multiple BAM...

exonAlignDepth-class: Class '"exonAlignDepth"': Align-depth data for single genes...

exonLoessModel-class: Class '"exonLoessModel"': Align-depth data for single genes...

extractBamRegions: extractBamRegions: Extraction of alignments from given...

extractGeneRegions: Extraction of alignments from given genetic regions and BAM...

extractRanges: extractRanges: Extraction of alignments

filename-methods: Reading 'filename' from bamReader or bamWriter

gapList-class: Class '"gapList"': Representation of genomic alignment gaps.

gapSiteList-class: Class '"gapSiteList"': Representation of genomic alignment...

geneAlignDepth-class: Class '"geneAlignDepth"': Align-depth data for single genes...

GenomePartition-class: Class '"GenomePartition"': .

getHeaderText-methods: 'getHeaderText' Assembling member data into Header-Text

getNextAlign-methods: 'getNextAlign': Retrieving next align from bamReader or...

getQualDf: Read and display Phred qualities from bamRange

getRefData: Retrieve reference sequence from a BAM file as data.frame

getVal: getVal(object,members): Retrieving values for given types...

groupRatio: Calculates group-wise ratios of alignment depth (AD)

headerLine-class: Class '"headerLine"': Representation of header line segment...

headerProgram-class: Class '"headerProgram"': Represention of header - program...

headerReadGroup-class: Class '"headerReadGroup"': Representation of read - group...

isOpen-methods: isOpen(bamReader), isOpen(bamWriter): Checking for opened...

multseq: Create combined sequences of sequential numbers.

nucStats: Table nucleotides in whole BAM file(s)

rangeSegCount-class: Class '"rangeSegCount"': Represents alignment counts in...

rangeToFastq: rangeToFastq: Extract read information from alignments for...

rbamtools-package: Reading, writing and manipulating BAM-file format.

readerToFastq: readerToFastq: Extraction of a subset of alignments from a...

readPooledBamGapDf: readPooledBamGapDf: Position data for alignments gaps from...

readPooledBamGaps: readPooledBamGaps: Position data for alignments gaps from...

refSeqDict-class: Class '"refSeqDict"': Repesentation of data from reference...

sampleBamFiles-class: Class '"sampleBamFiles"': Data on multiple BAM files from an...

saveAldData: saveAldData: Save alignment depth plots for single genes

segmentize: Segmentation of vector using segment coordinates

setVal: setVal(object,members,values): Setting values for given data...

Functions

addReadGroup Man page
addReadGroup,headerReadGroup-method Man page
addReadGroup-methods Man page
addSeq Man page
addSeq,refSeqDict-method Man page
aldRatio Man page
aldRatio,exonAlignDepth-method Man page
aldRatio-methods 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.bamGapList Man page
as.data.frame.bamRange Man page
as.data.frame.gapList Man page
as.data.frame.gapSiteList Man page
as.data.frame-methods Man page
as.data.frame.rangeSegCount Man page
as.data.frame.refSeqDict Man page
as.data.frame,refSeqDict-method 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,bamWriter-method Man page
bamCopy-methods Man page
bamCount Man page
bamCountAll Man page
bamCountAll,bamReader,ANY-method Man page
bamCountAll-methods Man page
bamCountAll,sampleBamFiles,logical-method Man page
bamCountAll,sampleBamFiles,missing-method Man page
bamCount,bamReader-method Man page
bamCount-methods Man page
bamFiles Man page
bamFiles<- Man page
bamFiles<--methods Man page
bamFiles-methods Man page
bamFiles<-,sampleBamFiles,character,logical-method Man page
bamFiles<-,sampleBamFiles,character-method Man page
bamFiles,sampleBamFiles-method 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
bamIdxFiles Man page
bamIdxFiles<- Man page
bamIdxFiles<--methods Man page
bamIdxFiles-methods Man page
bamIdxFiles<-,sampleBamFiles,character-method Man page
bamIdxFiles,sampleBamFiles-method Man page
bamRange Man page
[,bamRange,ANY,ANY,ANY-method Man page
bamRange-class Man page
bamReader Man page
bamReader-class Man page
bamSave Man page
bamSave,bamReader,ANY,ANY-method Man page
bamSave,bamReader,bamWriter,missing-method Man page
bamSave,bamReader-method Man page
bamSave,bamWriter,bamAlign,numeric-method Man page
bamSave,bamWriter,bamRange,character-method Man page
bamSave,bamWriter,bamRange,missing-method Man page
bamSave,bamWriter,bamRange,numeric-method Man page
bamSave,bamWriter-method Man page
bamSave-methods Man page
bamSort Man page
bamSort,bamReader,ANY,ANY,ANY-method Man page
bamSort,bamReader-method Man page
bamSort-methods Man page
bamSort,sampleBamFiles,ANY,ANY,ANY-method Man page
bamSort,sampleBamFiles-method Man page
bamWriter Man page
bamWriter,bamHeader-method Man page
bamWriter-class Man page
checkBamFiles Man page
checkBamFiles-methods Man page
checkBamFiles,sampleBamFiles-method Man page
checkPartition Man page
checkPartition,GenomePartition,data.frame-method Man page
checkPartition-methods Man page
cigarData Man page
cigarData,bamAlign-method Man page
cigarData-methods 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, rangeSegCount, 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
countPartition Man page
countPartition,GenomePartition,bamReader-method Man page
countPartition,GenomePartition,data.frame-method Man page
countPartition-methods Man page
countTextLines Man page
create.idx.batch Man page
createIdxBatch Man page
create.index Man page
createIndex Man page
createIndex,bamReader,character-method Man page
create.index,bamReader-method Man page
createIndex,bamReader,missing-method Man page
create.index-methods Man page
createIndex-methods Man page
createIndex,sampleBamFiles,character-method Man page
createIndex,sampleBamFiles,missing-method Man page
cutFlatAlignDepth Man page
cutFlatAlignDepth,exonAlignDepth-method Man page
cutFlatAlignDepth,exonLoessModel-method Man page
cutFlatAlignDepth-methods Man page
dim,refSeqDict-method Man page
exonAlignDepth Man page
[,exonAlignDepth,ANY,ANY,ANY-method Man page
exonAlignDepth-class Man page
exonAlignDepth,geneAlignDepth-method Man page
exonAlignDepth-methods Man page
exonLoessModel Man page
[,exonLoessModel,ANY,ANY,ANY-method Man page
exonLoessModel-class Man page
exonLoessModel,exonAlignDepth-method Man page
exonLoessModel-methods Man page
extractBamRegions Man page
extractGeneRegions Man page
extractGeneRegions,bamReader,bamWriter,geneList-method Man page
extractGeneRegions,bamReader,character,geneList-method Man page
extractGeneRegions-methods Man page
extractGeneRegions,sampleBamFiles,sampleBamFiles,geneList-method Man page
extractRanges Man page
extractRanges,bamReader-method Man page
extractRanges-methods Man page
failedQC Man page
failedQC<- Man page
failedQC<-,bamAlign-method Man page
failedQC,bamAlign-method Man page
failedQC<--methods 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<- Man page
firstInPair<-,bamAlign-method Man page
firstInPair,bamAlign-method Man page
firstInPair<--methods Man page
firstInPair-methods Man page
flag Man page
flag<- Man page
flag<-,bamAlign-method Man page
flag,bamAlign-method Man page
flag<--methods Man page
flag-methods Man page
gapList Man page
gapList,bamReader,numeric-method Man page
gapList-class Man page
gapSiteList-class Man page
geneAlignDepth Man page
[,geneAlignDepth,ANY,ANY,ANY-method Man page
geneAlignDepth-class Man page
geneAlignDepth-methods Man page
geneAlignDepth,sampleBamFiles,geneModel-method Man page
genomePartition Man page
genomePartition,bamReader,data.frame-method Man page
GenomePartition-class Man page
genomePartition-methods Man page
getAlignCounts Man page
getAlignCounts,GenomePartition-method Man page
getAlignCounts-methods 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
getFileTable Man page
getFileTable,GenomePartition-method Man page
getFileTable-methods Man page
getGridAlignCounts Man page
getGridAlignCounts,GenomePartition-method Man page
getGridAlignCounts-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-methods Man page
getHeaderText,refSeqDict-method Man page
getNextAlign Man page
getNextAlign,bamRange-method Man page
getNextAlign,bamReader-method Man page
getNextAlign-methods Man page
getNormFactor Man page
getNormFactor,exonAlignDepth-method Man page
getNormFactor-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,logical-method Man page
getQualDf,bamRange,missing-method Man page
getQualDf-methods Man page
getQualQuantiles Man page
getQualQuantiles,bamRange,numeric-method Man page
getQualQuantiles-methods Man page
getRefCoords Man page
getRefCoords,bamReader,character-method Man page
getRefCoords,bamReader,factor-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,bamWriter-method Man page
getRefData,GenomePartition-method Man page
getRefData-methods Man page
getRefId Man page
getRefId,bamReader,character-method Man page
getRefId,bamReader,factor-method Man page
getRefId,bamWriter,character-method Man page
getRefId,bamWriter,factor-method Man page
getRefId-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
getSeqNr Man page
getSeqNr,GenomePartition-method Man page
getSeqNr-methods Man page
getVal Man page
getVal,headerLine-method Man page
getVal,headerProgram-method Man page
getVal,headerReadGroup-method Man page
groupAldMatrix Man page
groupAldMatrix,exonAlignDepth-method Man page
groupAldMatrix-methods Man page
groupAldTable Man page
groupAldTable,exonAlignDepth-method Man page
groupAldTable-methods Man page
groupRatio Man page
groupRatio,exonLoessModel-method Man page
groupRatio-methods Man page
groupTable Man page
groupTable<- Man page
groupTable<--methods Man page
groupTable-methods Man page
groupTable<-,sampleBamFiles,character-method Man page
groupTable<-,sampleBamFiles,data.frame-method Man page
groupTable,sampleBamFiles-method Man page
head Man page
headerLine Man page
headerLine<- Man page
headerLine<-,bamHeaderText-method Man page
headerLine,bamHeaderText-method Man page
headerLine-class Man page
headerProgram Man page
headerProgram<- Man page
headerProgram<-,bamHeaderText-method Man page
headerProgram,bamHeaderText-method Man page
headerProgram-class Man page
headerReadGroup Man page
headerReadGroup<- Man page
headerReadGroup<-,bamHeaderText-method Man page
headerReadGroup,bamHeaderText-method Man page
headerReadGroup-class Man page
head,refSeqDict-method Man page
index.initialized Man page
indexInitialized Man page
index.initialized,bamReader-method Man page
indexInitialized,bamReader-method Man page
index.initialized-methods Man page
indexInitialized-methods 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, exonAlignDepth Man page
initialize, exonLoessModel Man page
initialize,gapList-method Man page
initialize,gapSiteList-method Man page
initialize, geneAlignDepth Man page
initialize,headerLine-method Man page
initialize,headerProgram-method Man page
initialize,headerReadGroup-method Man page
initialize, rangeSegCount-method Man page
initialize,refSeqDict-method Man page
initialize, sampleBamFiles 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
junctionSites Man page
junctionSites,exonAlignDepth-method Man page
junctionSites-methods Man page
length,exonAlignDepth-method Man page
length,exonLoessModel-method Man page
length,geneAlignDepth-method Man page
length,sampleBamFiles-method Man page
load.index Man page
loadIndex Man page
load.index,bamReader-method Man page
loadIndex,bamReader-method Man page
load.index-methods 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<- Man page
mateReverseStrand<-,bamAlign-method Man page
mateReverseStrand,bamAlign-method Man page
mateReverseStrand<--methods Man page
mateReverseStrand-methods Man page
mateUnmapped Man page
mateUnmapped<- Man page
mateUnmapped<-,bamAlign-method Man page
mateUnmapped,bamAlign-method Man page
mateUnmapped<--methods Man page
mateUnmapped-methods Man page
meltDownSegments Man page
meltDownSegments-methods Man page
meltDownSegments,rangeSegCount-method Man page
merge.bamGapList Man page
merge.gapSiteList Man page
[-methods Man page
moveCurrentAlign Man page
moveCurrentAlign,bamRange-method Man page
moveCurrentAlign-methods Man page
multSeq 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<- Man page
nAligns,bamGapList-method Man page
nAligns,gapList-method Man page
nAligns,gapSiteList-method Man page
nAligns<--methods Man page
nAligns-methods Man page
nAligns<-,sampleBamFiles,character,numeric-method Man page
nAligns<-,sampleBamFiles,integer-method Man page
nAligns,sampleBamFiles-method Man page
nAligns<-,sampleBamFiles,numeric-method Man page
name Man page
name,bamAlign-method Man page
name-methods Man page
nCigar Man page
nCigar,bamAlign-method Man page
nCigar-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<- Man page
paired<-,bamAlign-method Man page
paired,bamAlign-method Man page
paired<--methods Man page
paired-methods Man page
pcrORopt_duplicate Man page
pcrORopt_duplicate<- Man page
pcrORopt_duplicate<-,bamAlign-method Man page
pcrORopt_duplicate,bamAlign-method Man page
pcrORopt_duplicate<--methods 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<- Man page
properPair<-,bamAlign-method Man page
properPair,bamAlign-method Man page
properPair<--methods 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
rangeSegCount Man page
rangeSegCount,bamReader-method Man page
rangeSegCount-class Man page
rangeSegCount-methods Man page
rangeToFastq Man page
rangeToFastq,bamRange,character-method Man page
rangeToFastq-methods Man page
rbamtools Man page
rbamtools-package 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
readPooledBamGapDf Man page
readPooledBamGaps Man page
readRange Man page
readRange,bamReader,character,numeric,logical-method Man page
readRange,bamReader,character,numeric,missing-method Man page
readRange,bamReader,factor,numeric,logical-method Man page
readRange,bamReader,factor,numeric,missing-method Man page
readRange-methods Man page
refID Man page
refID<- Man page
refID,bamAlign-method Man page
refID,gapSiteList-method Man page
refID<-,gapSiteList,numeric-method Man page
refID<--methods Man page
refID-methods Man page
refSeqDict Man page
refSeqDict<- Man page
[,refSeqDict,ANY,ANY,ANY-method Man page
refSeqDict<-,bamHeaderText-method Man page
refSeqDict,bamHeaderText-method Man page
refSeqDict-class Man page
[<-,refSeqDict-method Man page
removeSeqs Man page
removeSeqs,refSeqDict-method Man page
reverseStrand Man page
reverseStrand<- Man page
reverseStrand<-,bamAlign-method Man page
reverseStrand,bamAlign-method Man page
reverseStrand<--methods Man page
reverseStrand-methods Man page
rewind Man page
rewind,bamRange-method Man page
rewind,bamReader-method Man page
rewind-methods Man page
sampleBamFiles Man page
[,sampleBamFiles,ANY,ANY,ANY-method Man page
sampleBamFiles,character-method Man page
sampleBamFiles-class Man page
sampleBamFiles,factor-method Man page
sampleBamFiles,integer-method Man page
sampleBamFiles-methods Man page
sampleBamFiles,numeric-method Man page
sampleGroups Man page
sampleGroups<- Man page
sampleGroups<--methods Man page
sampleGroups-methods Man page
sampleGroups<-,sampleBamFiles,character-method Man page
sampleGroups<-,sampleBamFiles,factor-method Man page
sampleGroups,sampleBamFiles-method Man page
sampleLabels Man page
sampleLabels<- Man page
sampleLabels<--methods Man page
sampleLabels-methods Man page
sampleLabels<-,sampleBamFiles,character-method Man page
sampleLabels<-,sampleBamFiles,factor-method Man page
sampleLabels<-,sampleBamFiles,integer-method Man page
sampleLabels,sampleBamFiles-method Man page
saveAldData Man page
saveAldData-methods Man page
saveAldData,sampleBamFiles,geneList-method Man page
secondaryAlign Man page
secondaryAlign<- Man page
secondaryAlign<-,bamAlign-method Man page
secondaryAlign,bamAlign-method Man page
secondaryAlign<--methods Man page
secondaryAlign-methods Man page
secondInPair Man page
secondInPair<- Man page
secondInPair<-,bamAlign-method Man page
secondInPair,bamAlign-method Man page
secondInPair<--methods Man page
secondInPair-methods Man page
segmentize Man page
segmentize,ANY-method Man page
segmentize,data.frame-method Man page
segmentize,matrix-method Man page
segmentize-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,exonAlignDepth-method Man page
show,exonLoessModel-method Man page
show,gapList-method Man page
show,gapSiteList-method Man page
show,geneAlignDepth-method Man page
show,GenomePartition-method Man page
show,sampleBamFiles-method Man page
siteList Man page
siteList,bamRange,missing-method Man page
siteList,bamReader,numeric-method Man page
siteList,missing,missing-method Man page
siteList,numeric,missing-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
size,rangeSegCount-method 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<- Man page
suppAlign<-,bamAlign-method Man page
suppAlign,bamAlign-method Man page
suppAlign<--methods Man page
suppAlign-methods Man page
tail Man page
tail,refSeqDict-method Man page
unmapped Man page
unmapped<- Man page
unmapped<-,bamAlign-method Man page
unmapped,bamAlign-method Man page
unmapped<--methods Man page
unmapped-methods Man page
writeCurrentAlign Man page
writeCurrentAlign,bamRange-method Man page
writeCurrentAlign-methods Man page

Files

rbamtools
rbamtools/inst
rbamtools/inst/extdata
rbamtools/inst/extdata/accepted_hits.bam.bai
rbamtools/inst/extdata/test.fastq
rbamtools/inst/extdata/accepted_hits.bam
rbamtools/inst/doc
rbamtools/inst/doc/rbamtools.pdf
rbamtools/inst/doc/rbamtools.R
rbamtools/inst/doc/rbamtools.Rnw
rbamtools/tests
rbamtools/tests/test-all.R
rbamtools/src
rbamtools/src/gap_list.h
rbamtools/src/Makevars
rbamtools/src/align_list.h
rbamtools/src/gapSiteList.h
rbamtools/src/grange.h
rbamtools/src/bitmask.h
rbamtools/src/range_partition.h
rbamtools/src/gapSiteListList.h
rbamtools/src/samtools
rbamtools/src/samtools/bam_index.c
rbamtools/src/samtools/bam_endian.h
rbamtools/src/samtools/sam.h
rbamtools/src/samtools/sam_header.c
rbamtools/src/samtools/bam_aux.c
rbamtools/src/samtools/kstring.c
rbamtools/src/samtools/bgzf.c
rbamtools/src/samtools/bgzf.h
rbamtools/src/samtools/ksort.h
rbamtools/src/samtools/bam_import.c
rbamtools/src/samtools/bam_sort.c
rbamtools/src/samtools/bam.c
rbamtools/src/samtools/sam.c
rbamtools/src/samtools/kseq.h
rbamtools/src/samtools/khash.h
rbamtools/src/samtools/faidx.c
rbamtools/src/samtools/razf.c
rbamtools/src/samtools/razf.h
rbamtools/src/samtools/LICENSE
rbamtools/src/samtools/kstring.h
rbamtools/src/samtools/faidx.h
rbamtools/src/samtools/rdef.h
rbamtools/src/samtools/bam.h
rbamtools/src/samtools/sam_header.h
rbamtools/src/rbamtools.h
rbamtools/src/align_counts.h
rbamtools/src/data_frame.h
rbamtools/src/Makevars.win
rbamtools/src/rbamtools.cpp
rbamtools/src/extptr.h
rbamtools/NAMESPACE
rbamtools/NEWS
rbamtools/R
rbamtools/R/segmentize.R rbamtools/R/sampleBamFiles.R rbamtools/R/rbamtools.R
rbamtools/vignettes
rbamtools/vignettes/rbamtools.bib
rbamtools/vignettes/rbamtools.Rnw
rbamtools/MD5
rbamtools/build
rbamtools/build/vignette.rds
rbamtools/DESCRIPTION
rbamtools/ChangeLog
rbamtools/man
rbamtools/man/bamCountAll.Rd rbamtools/man/groupRatio.Rd rbamtools/man/countTextLines.Rd rbamtools/man/countNucs.Rd rbamtools/man/getNextAlign-methods.Rd rbamtools/man/rangeSegCount-class.Rd rbamtools/man/rbamtools-package.Rd rbamtools/man/refSeqDict-class.Rd rbamtools/man/createIdxBatch.Rd rbamtools/man/bamClose-methods.Rd rbamtools/man/multseq.Rd rbamtools/man/GenomePartition-class.Rd rbamtools/man/bamSave.Rd rbamtools/man/bamCount.Rd rbamtools/man/geneAlignDepth-class.Rd rbamtools/man/isOpen-methods.Rd rbamtools/man/extractBamRegions.Rd rbamtools/man/getQualDf.Rd rbamtools/man/segmentize.Rd rbamtools/man/headerReadGroup-class.Rd rbamtools/man/readPooledBamGapDf.Rd rbamtools/man/bamHeaderText-class.Rd rbamtools/man/getVal.Rd rbamtools/man/exonAlignDepth-class.Rd rbamtools/man/gapList-class.Rd rbamtools/man/nucStats.Rd rbamtools/man/getHeaderText-methods.Rd rbamtools/man/bamAlign-class.Rd rbamtools/man/readPooledBamGaps.Rd rbamtools/man/headerProgram-class.Rd rbamtools/man/bamSort.Rd rbamtools/man/bamGapList-class.Rd rbamtools/man/alignDepth-class.Rd rbamtools/man/rangeToFastq.Rd rbamtools/man/bamWriter-class.Rd rbamtools/man/gapSiteList-class.Rd rbamtools/man/exonLoessModel-class.Rd rbamtools/man/bamWriter.Rd rbamtools/man/bamRange-class.Rd rbamtools/man/setVal.Rd rbamtools/man/readerToFastq.Rd rbamtools/man/bamReader-class.Rd rbamtools/man/bamAlign.Rd rbamtools/man/bamHeader-class.Rd rbamtools/man/extractGeneRegions.Rd rbamtools/man/extractRanges.Rd rbamtools/man/bamReader.Rd rbamtools/man/getRefData.Rd rbamtools/man/filename-methods.Rd rbamtools/man/saveAldData.Rd rbamtools/man/headerLine-class.Rd rbamtools/man/bamRange.Rd rbamtools/man/as.data.frame-methods.Rd rbamtools/man/sampleBamFiles-class.Rd

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