| 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.rangeSegCount |
Class '"rangeSegCount"': Represents alignment counts in segments of genetic regions. |
| 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(object, 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. |
| 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. |
| 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 '"rangeSegCount"': Represents alignment counts in segments of genetic regions. |
| 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 |
rangeToFastq: Extract read information from alignments for given genomic range as fastq. |
| range2fastq-method |
rangeToFastq: Extract read information from alignments for given genomic range as fastq. |
| range2fastq-methods |
rangeToFastq: Extract read information from alignments for given genomic range as fastq. |
| rangeSegCount |
Class '"rangeSegCount"': Represents alignment counts in segments of genetic regions. |
| rangeSegCount-class |
Class '"rangeSegCount"': Represents alignment counts in segments of genetic regions. |
| rangeSegCount-method |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
| rangeSegCount-methods |
Class '"bamReader"': Representation for file connection to BAM file for reading access. |
| rangeToFastq |
rangeToFastq: Extract read information from alignments for given genomic range as fastq. |
| rangeToFastq-method |
rangeToFastq: Extract read information from alignments for given genomic range as fastq. |
| rangeToFastq-methods |
rangeToFastq: Extract read information from alignments for given genomic range as fastq. |
| rbamtools |
Reading, writing and manipulating BAM-file format. |
| reader2fastq |
readerToFastq: Extraction of a subset of alignments from a BAM files into fastq format. |
| reader2fastq-method |
readerToFastq: Extraction of a subset of alignments from a BAM files into fastq format. |
| reader2fastq-methods |
readerToFastq: Extraction of a subset of alignments from a BAM files into fastq format. |
| readerToFastq |
readerToFastq: Extraction of a subset of alignments from a BAM files into fastq format. |
| readerToFastq-method |
readerToFastq: Extraction of a subset of alignments from a BAM files into fastq format. |
| readerToFastq-methods |
readerToFastq: 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 '"GenomePartition"': . |
| 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-method |
Class '"rangeSegCount"': Represents alignment counts in segments of genetic regions. |
| 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. |