addReadGroup |
Class '"headerReadGroup"': Representation of read - group data in header section of BAM files |
addReadGroup-method |
Class '"headerReadGroup"': Representation of read - group data in header section of BAM files |
addReadGroup-methods |
Class '"headerReadGroup"': Representation of read - group data in header section of BAM files |
addSeq |
Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header. |
addSeq-method |
Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header. |
alignDepth |
Class '"alignDepth"': Alignment depth information from bamRange objects. |
alignDepth-class |
Class '"alignDepth"': Alignment depth information from bamRange objects. |
alignDepth-method |
Class '"alignDepth"': Alignment depth information from bamRange objects. |
alignDepth-methods |
Class '"alignDepth"': Alignment depth information from bamRange objects. |
alignQual |
Class '"bamAlign"': Representation of single genomic alignments. |
alignQual-method |
Class '"bamAlign"': Representation of single genomic alignments. |
alignQual-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
alignQualVal |
Class '"bamAlign"': Representation of single genomic alignments. |
alignQualVal-method |
Class '"bamAlign"': Representation of single genomic alignments. |
alignQualVal-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
alignSeq |
Class '"bamAlign"': Representation of single genomic alignments. |
alignSeq-method |
Class '"bamAlign"': Representation of single genomic alignments. |
alignSeq-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
as.character |
Class '"bamHeader"': Representation of data contained in the header section of BAM files. |
as.character-method |
Class '"bamHeader"': Representation of data contained in the header section of BAM files. |
as.data.frame-method |
Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header. |
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"': Representation of genomic alignments in defined regions. |
as.data.frame.gapList |
Class '"gapList"': Representation of genomic alignment gaps. |
as.data.frame.gapSiteList |
Class '"gapSiteList"': Representation of genomic alignment gap positions. |
as.data.frame.refSeqDict |
Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header. |
as.list-method |
Class '"headerLine"': Representation of header line segment of header section for BAM files. |
as.list-method |
Class '"headerProgram"': Represention of header - program section of BAM header. |
as.list-method |
Class '"headerReadGroup"': Representation of read - group data in header section of BAM files |
bamAlign |
bamAlign |
bamAlign-class |
Class '"bamAlign"': Representation of single genomic alignments. |
bamClose |
bamClose(bamReader), bamClose(bamWriter): Closing of file connections. |
bamClose-method |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
bamClose-method |
Class '"bamWriter"': Representation of a file connection to a BAM file for writing access. |
bamClose-methods |
bamClose(bamReader), bamClose(bamWriter): Closing of file connections. |
bamCopy |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
bamCopy-method |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
bamCopy-methods |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
bamCount |
bamCount: Counting of CIGAR-OP items |
bamCount-method |
bamCount: Counting of CIGAR-OP items |
bamCount-methods |
bamCount: Counting of CIGAR-OP items |
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"': Representation of data contained in the header section of BAM files. |
bamHeader-class |
Class '"bamHeader"': Representation of data contained in the header section of BAM files. |
bamHeader-method |
Class '"bamHeader"': Textual representation of header section of BAM files. |
bamHeaderText |
Class '"bamHeader"': Textual representation of header section of BAM files. |
bamHeaderText-class |
Class '"bamHeader"': Textual representation of header section of BAM files. |
bamRange |
bamRange(bamReader, coordinates,complex=FALSE): Function for reading of alignments in genomic regions. |
bamRange-class |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
bamReader |
bamReader: Connection to BAM file for reading access. |
bamReader-class |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
bamSave |
Class '"bamWriter"': Representation of a file connection to a BAM file for writing access. |
bamSave-method |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
bamSave-method |
Class '"bamWriter"': Representation of a file connection to a BAM file for writing access. |
bamSave-methods |
Class '"bamWriter"': Representation of a file connection to a BAM file for writing access. |
bamSort |
bamSort: Creation of a sorted copy of a BAM file. |
bamSort-method |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
bamWriter |
bamWriter: Opening a file connection to a BAM file for writing access. |
bamWriter-class |
Class '"bamWriter"': Representation of a file connection to a BAM file for writing access. |
bamWriter-method |
Class '"bamHeader"': Representation of data contained in the header section of BAM files. |
cigarData |
Class '"bamAlign"': Representation of single genomic alignments. |
cigarData-method |
Class '"bamAlign"': Representation of single genomic alignments. |
cigarData-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
coerce-method |
Class '"bamGapList"' |
coerce-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
coerce-method |
Class '"gapList"': Representation of genomic alignment gaps. |
coerce-method |
Class '"gapSiteList"': Representation of genomic alignment gap positions. |
coerce-method |
Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header. |
countNucs |
Counting nucleotides in 'bamAlign' and 'bamRange' |
countNucs-method |
Counting nucleotides in 'bamAlign' and 'bamRange' |
countNucs-methods |
Counting nucleotides in 'bamAlign' and 'bamRange' |
countTextLines |
countTextLines: Counting lines in text files. |
create.idx.batch |
createIdxBatch: Creation of index files for multiple BAM files. |
create.index |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
create.index-method |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
create.index-methods |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
createIdxBatch |
createIdxBatch: Creation of index files for multiple BAM files. |
createIndex |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
createIndex-method |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
createIndex-methods |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
failedQC |
Class '"bamAlign"': Representation of single genomic alignments. |
failedQC-method |
Class '"bamAlign"': Representation of single genomic alignments. |
failedQC-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
failedQC<- |
Class '"bamAlign"': Representation of single genomic alignments. |
failedQC<--method |
Class '"bamAlign"': Representation of single genomic alignments. |
failedQC<--methods |
Class '"bamAlign"': Representation of single genomic alignments. |
filename |
Reading 'filename' from bamReader or bamWriter |
filename-method |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
filename-method |
Class '"bamWriter"': Representation of a file connection to a BAM file for writing access. |
filename-methods |
Reading 'filename' from bamReader or bamWriter |
firstInPair |
Class '"bamAlign"': Representation of single genomic alignments. |
firstInPair-method |
Class '"bamAlign"': Representation of single genomic alignments. |
firstInPair-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
firstInPair<- |
Class '"bamAlign"': Representation of single genomic alignments. |
firstInPair<--method |
Class '"bamAlign"': Representation of single genomic alignments. |
firstInPair<--methods |
Class '"bamAlign"': Representation of single genomic alignments. |
flag |
Class '"bamAlign"': Representation of single genomic alignments. |
flag-method |
Class '"bamAlign"': Representation of single genomic alignments. |
flag-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
flag<- |
Class '"bamAlign"': Representation of single genomic alignments. |
flag<--method |
Class '"bamAlign"': Representation of single genomic alignments. |
flag<--methods |
Class '"bamAlign"': Representation of single genomic alignments. |
gapList |
Class '"gapList"': Representation of genomic alignment gaps. |
gapList-class |
Class '"gapList"': Representation of genomic alignment gaps. |
gapList-method |
Class '"gapList"': Representation of genomic alignment gaps. |
gapSiteList-class |
Class '"gapSiteList"': Representation of genomic alignment gap positions. |
getAlignRange |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getAlignRange-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getAlignRange-methods |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getCoords |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getCoords-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getCoords-methods |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getDepth |
Class '"alignDepth"': Alignment depth information from bamRange objects. |
getDepth-method |
Class '"alignDepth"': Alignment depth information from bamRange objects. |
getDepth-methods |
Class '"alignDepth"': Alignment depth information from bamRange objects. |
getHeader |
Class '"bamHeader"': Textual representation of header section of BAM files. |
getHeader-method |
Class '"bamHeader"': Textual representation of header section of BAM files. |
getHeader-method |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
getHeaderText |
'getHeaderText' Assembling member data into Header-Text |
getHeaderText-method |
Class '"bamHeader"': Representation of data contained in the header section of BAM files. |
getHeaderText-method |
Class '"bamHeader"': Textual representation of header section of BAM files. |
getHeaderText-method |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
getHeaderText-method |
Class '"headerLine"': Representation of header line segment of header section for BAM files. |
getHeaderText-method |
Class '"headerProgram"': Represention of header - program section of BAM header. |
getHeaderText-method |
Class '"headerReadGroup"': Representation of read - group data in header section of BAM files |
getHeaderText-method |
Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header. |
getHeaderText-methods |
'getHeaderText' Assembling member data into Header-Text |
getNextAlign |
'getNextAlign': Retrieving next align from bamReader or bamRange |
getNextAlign-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getNextAlign-method |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
getNextAlign-methods |
'getNextAlign': Retrieving next align from bamReader or bamRange |
getParams |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getParams-method |
Class '"alignDepth"': Alignment depth information from bamRange objects. |
getParams-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getParams-methods |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getPos |
Class '"alignDepth"': Alignment depth information from bamRange objects. |
getPos-method |
Class '"alignDepth"': Alignment depth information from bamRange objects. |
getPos-methods |
Class '"alignDepth"': Alignment depth information from bamRange objects. |
getPrevAlign |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getPrevAlign-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getPrevAlign-methods |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
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 |
Retrieve reference sequence from a BAM file as data.frame |
getRefCoords-method |
Retrieve reference sequence from a BAM file as data.frame |
getRefCoords-methods |
Retrieve reference sequence from a BAM file as data.frame |
getRefCount |
Retrieve reference sequence from a BAM file as data.frame |
getRefCount-method |
Retrieve reference sequence from a BAM file as data.frame |
getRefCount-methods |
Retrieve reference sequence from a BAM file as data.frame |
getRefData |
Retrieve reference sequence from a BAM file as data.frame |
getRefData-method |
Retrieve reference sequence from a BAM file as data.frame |
getRefData-methods |
Retrieve reference sequence from a BAM file as data.frame |
getRefName |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getRefName-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getRefName-methods |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getSeqLen |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getSeqLen-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getSeqLen-methods |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
getVal |
getVal(object,members): Retrieving values for given types from an object |
getVal-method |
Class '"headerLine"': Representation of header line segment of header section for BAM files. |
getVal-method |
Class '"headerProgram"': Represention of header - program section of BAM header. |
getVal-method |
Class '"headerReadGroup"': Representation of read - group data in header section of BAM files |
head |
Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header. |
head-method |
Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header. |
headerLine |
Class '"bamHeader"': Textual representation of header section of BAM files. |
headerLine-class |
Class '"headerLine"': Representation of header line segment of header section for BAM files. |
headerLine-method |
Class '"bamHeader"': Textual representation of header section of BAM files. |
headerLine<- |
Class '"bamHeader"': Textual representation of header section of BAM files. |
headerLine<--method |
Class '"bamHeader"': Textual representation of header section of BAM files. |
headerProgram |
Class '"bamHeader"': Textual representation of header section of BAM files. |
headerProgram-class |
Class '"headerProgram"': Represention of header - program section of BAM header. |
headerProgram-method |
Class '"bamHeader"': Textual representation of header section of BAM files. |
headerProgram<- |
Class '"bamHeader"': Textual representation of header section of BAM files. |
headerProgram<--method |
Class '"bamHeader"': Textual representation of header section of BAM files. |
headerReadGroup |
Class '"bamHeader"': Textual representation of header section of BAM files. |
headerReadGroup-class |
Class '"headerReadGroup"': Representation of read - group data in header section of BAM files |
headerReadGroup-method |
Class '"bamHeader"': Textual representation of header section of BAM files. |
headerReadGroup<- |
Class '"bamHeader"': Textual representation of header section of BAM files. |
headerReadGroup<--method |
Class '"bamHeader"': Textual representation of header section of BAM files. |
index.initialized |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
index.initialized-method |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
index.initialized-methods |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
indexInitialized |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
indexInitialized-method |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
indexInitialized-methods |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
initialize-method |
Class '"bamAlign"': Representation of single genomic alignments. |
initialize-method |
Class '"bamGapList"' |
initialize-method |
Class '"bamHeader"': Representation of data contained in the header section of BAM files. |
initialize-method |
Class '"bamHeader"': Textual representation of header section of BAM files. |
initialize-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
initialize-method |
Class '"bamWriter"': Representation of a file connection to a BAM file for writing access. |
initialize-method |
Class '"gapList"': Representation of genomic alignment gaps. |
initialize-method |
Class '"gapSiteList"': Representation of genomic alignment gap positions. |
initialize-method |
Class '"headerLine"': Representation of header line segment of header section for BAM files. |
initialize-method |
Class '"headerProgram"': Represention of header - program section of BAM header. |
initialize-method |
Class '"headerReadGroup"': Representation of read - group data in header section of BAM files |
initialize-method |
Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header. |
insertPastCurrent |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
insertPastCurrent-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
insertPastCurrent-methods |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
insertPreCurrent |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
insertPreCurrent-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
insertPreCurrent-methods |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
insertSize |
Class '"bamAlign"': Representation of single genomic alignments. |
insertSize-method |
Class '"bamAlign"': Representation of single genomic alignments. |
insertSize-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
isOpen |
isOpen(bamReader), isOpen(bamWriter): Checking for opened file connection to BAM file. |
isOpen-method |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
isOpen-method |
Class '"bamWriter"': Representation of a file connection to a BAM file for writing access. |
isOpen-methods |
isOpen(bamReader), isOpen(bamWriter): Checking for opened file connection to BAM file. |
nAlignGaps |
Class '"gapList"': Representation of genomic alignment gaps. |
nAlignGaps-method |
Class '"bamGapList"' |
nAlignGaps-method |
Class '"gapList"': Representation of genomic alignment gaps. |
nAlignGaps-method |
Class '"gapSiteList"': Representation of genomic alignment gap positions. |
nAlignGaps-methods |
Class '"gapList"': Representation of genomic alignment gaps. |
nAligns |
Class '"gapList"': Representation of genomic alignment gaps. |
nAligns-method |
Class '"bamGapList"' |
nAligns-method |
Class '"gapList"': Representation of genomic alignment gaps. |
nAligns-method |
Class '"gapSiteList"': Representation of genomic alignment gap positions. |
nAligns-methods |
Class '"gapList"': Representation of genomic alignment gaps. |
name |
Class '"bamAlign"': Representation of single genomic alignments. |
name-method |
Class '"bamAlign"': Representation of single genomic alignments. |
name-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
nCigar |
Class '"bamAlign"': Representation of single genomic alignments. |
nCigar-method |
Class '"bamAlign"': Representation of single genomic alignments. |
nCigar-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
nucStats |
Table nucleotides in whole BAM file(s) |
nucStats-method |
Table nucleotides in whole BAM file(s) |
nucStats-methods |
Table nucleotides in whole BAM file(s) |
paired |
Class '"bamAlign"': Representation of single genomic alignments. |
paired-method |
Class '"bamAlign"': Representation of single genomic alignments. |
paired-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
paired<- |
Class '"bamAlign"': Representation of single genomic alignments. |
paired<--method |
Class '"bamAlign"': Representation of single genomic alignments. |
paired<--methods |
Class '"bamAlign"': Representation of single genomic alignments. |
pcrORopt_duplicate |
Class '"bamAlign"': Representation of single genomic alignments. |
pcrORopt_duplicate-method |
Class '"bamAlign"': Representation of single genomic alignments. |
pcrORopt_duplicate-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
pcrORopt_duplicate<- |
Class '"bamAlign"': Representation of single genomic alignments. |
pcrORopt_duplicate<--method |
Class '"bamAlign"': Representation of single genomic alignments. |
pcrORopt_duplicate<--methods |
Class '"bamAlign"': Representation of single genomic alignments. |
plotAlignDepth |
Class '"alignDepth"': Alignment depth information from bamRange objects. |
plotAlignDepth-method |
Class '"alignDepth"': Alignment depth information from bamRange objects. |
plotAlignDepth-methods |
Class '"alignDepth"': Alignment depth information from bamRange objects. |
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"': Representation of genomic alignments in defined regions. |
pop_back-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
pop_back-methods |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
pop_front |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
pop_front-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
pop_front-methods |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
position |
Class '"bamAlign"': Representation of single genomic alignments. |
position-method |
Class '"bamAlign"': Representation of single genomic alignments. |
position-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
properPair |
Class '"bamAlign"': Representation of single genomic alignments. |
properPair-method |
Class '"bamAlign"': Representation of single genomic alignments. |
properPair-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
properPair<- |
Class '"bamAlign"': Representation of single genomic alignments. |
properPair<--method |
Class '"bamAlign"': Representation of single genomic alignments. |
properPair<--methods |
Class '"bamAlign"': Representation of single genomic alignments. |
push_back |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
push_back-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
push_back-methods |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
push_front |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
push_front-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
push_front-methods |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
range2fastq |
range2fastq: Extract read information from alignments for given genomic range as fastq. |
range2fastq-method |
range2fastq: Extract read information from alignments for given genomic range as fastq. |
range2fastq-methods |
range2fastq: Extract read information from alignments for given genomic range as fastq. |
rbamtools |
Reading, writing and manipulating BAM-file format. |
reader2fastq |
reader2fastq: Extraction of a subset of alignments from a BAM files into fastq format. |
reader2fastq-method |
reader2fastq: Extraction of a subset of alignments from a BAM files into fastq format. |
reader2fastq-methods |
reader2fastq: Extraction of a subset of alignments from a BAM files into fastq format. |
readPooledBamGapDf |
readPooledBamGapDf: Position data for alignments gaps from multiple BAM files. |
readPooledBamGaps |
readPooledBamGaps: Position data for alignments gaps from multiple BAM files. |
refID |
Class '"bamAlign"': Representation of single genomic alignments. |
refID-method |
Class '"bamAlign"': Representation of single genomic alignments. |
refID-method |
Class '"gapSiteList"': Representation of genomic alignment gap positions. |
refID-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
refSeqDict |
Class '"bamHeader"': Textual representation of header section of BAM files. |
refSeqDict-class |
Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header. |
refSeqDict-method |
Class '"bamHeader"': Textual representation of header section of BAM files. |
refSeqDict<- |
Class '"bamHeader"': Textual representation of header section of BAM files. |
refSeqDict<--method |
Class '"bamHeader"': Textual representation of header section of BAM files. |
removeSeqs |
Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header. |
removeSeqs-method |
Class '"refSeqDict"': Repesentation of data from reference sequence dictionary in BAM file header. |
reverseStrand |
Class '"bamAlign"': Representation of single genomic alignments. |
reverseStrand-method |
Class '"bamAlign"': Representation of single genomic alignments. |
reverseStrand-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
reverseStrand<- |
Class '"bamAlign"': Representation of single genomic alignments. |
reverseStrand<--method |
Class '"bamAlign"': Representation of single genomic alignments. |
reverseStrand<--methods |
Class '"bamAlign"': Representation of single genomic alignments. |
rewind |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
rewind-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
rewind-method |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
rewind-methods |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
secondaryAlign |
Class '"bamAlign"': Representation of single genomic alignments. |
secondaryAlign-method |
Class '"bamAlign"': Representation of single genomic alignments. |
secondaryAlign-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
secondaryAlign<- |
Class '"bamAlign"': Representation of single genomic alignments. |
secondaryAlign<--method |
Class '"bamAlign"': Representation of single genomic alignments. |
secondaryAlign<--methods |
Class '"bamAlign"': Representation of single genomic alignments. |
secondInPair |
Class '"bamAlign"': Representation of single genomic alignments. |
secondInPair-method |
Class '"bamAlign"': Representation of single genomic alignments. |
secondInPair-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
secondInPair<- |
Class '"bamAlign"': Representation of single genomic alignments. |
secondInPair<--method |
Class '"bamAlign"': Representation of single genomic alignments. |
secondInPair<--methods |
Class '"bamAlign"': Representation of single genomic alignments. |
setVal |
setVal(object,members,values): Setting values for given data items |
setVal-method |
Class '"headerLine"': Representation of header line segment of header section for BAM files. |
setVal-method |
Class '"headerProgram"': Represention of header - program section of BAM header. |
setVal-method |
Class '"headerReadGroup"': Representation of read - group data in header section of BAM files |
show-method |
Class '"alignDepth"': Alignment depth information from bamRange objects. |
show-method |
Class '"bamGapList"' |
show-method |
Class '"bamHeader"': Representation of data contained in the header section of BAM files. |
show-method |
Class '"gapList"': Representation of genomic alignment gaps. |
show-method |
Class '"gapSiteList"': Representation of genomic alignment gap positions. |
siteList |
Class '"gapSiteList"': Representation of genomic alignment gap positions. |
siteList-method |
Class '"gapSiteList"': Representation of genomic alignment gap positions. |
size |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
size-method |
Class '"bamGapList"' |
size-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
size-method |
Class '"gapList"': Representation of genomic alignment gaps. |
size-method |
Class '"gapSiteList"': Representation of genomic alignment gap positions. |
size-methods |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
stepNextAlign |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
stepNextAlign-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
stepNextAlign-methods |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
stepPrevAlign |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
stepPrevAlign-method |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
stepPrevAlign-methods |
Class '"bamRange"': Representation of genomic alignments in defined regions. |
summary.bamGapList |
Class '"bamGapList"' |
suppAlign |
Class '"bamAlign"': Representation of single genomic alignments. |
suppAlign-method |
Class '"bamAlign"': Representation of single genomic alignments. |
suppAlign-methods |
Class '"bamAlign"': Representation of single genomic alignments. |
suppAlign<- |
Class '"bamAlign"': Representation of single genomic alignments. |
suppAlign<--method |
Class '"bamAlign"': Representation of single genomic alignments. |
suppAlign<--methods |
Class '"bamAlign"': Representation of single genomic alignments. |