| .BamFile_guessIndex |
Source code
|
| .BamViews_delegate |
Source code
|
| .BamViews_which |
Source code
|
| .RsamtoolsFile |
Source code
|
| .ScanBcfParam |
Source code
|
| .apply_bin_levels |
Source code
|
| .as.data.frame_list_of_lists |
Source code
|
| .as.factor_bin |
Source code
|
| .as.list_PileupParam |
Source code
|
| .ascii_offset |
Source code
|
| .bcfHeaderAsSimpleList |
Source code
|
| .bcf_template |
Source code
|
| .bin_levels |
Source code
|
| .build_path |
Source code
|
| .calcBitPos |
Source code
|
| .checkPrefixSuffix |
Source code
|
| .check_qname_arg |
Source code
|
| .countBam_postprocess |
Source code
|
| .detailedSummary |
Source code
|
| .extptr |
Source code
|
| .file.rename |
Source code
|
| .filterBam_FilterRules |
Source code
|
| .filterBam_preprocess |
Source code
|
| .findMateWithinGroups |
Source code
|
| .has.wholenumbers |
Source code
|
| .headerTabix |
Source code
|
| .io_bam |
Source code
|
| .io_bcf |
Source code
|
| .io_check_exists |
Source code
|
| .isValidHit |
Source code
|
| .load_bamcols_from_scanBam_res |
Source code
|
| .make_unique |
Source code
|
| .metacols_run_lengths |
Source code
|
| .normalizePath |
Source code
|
| .normalizeRangesList |
Source code
|
| .normalize_tagFilter |
Source code
|
| .onLoad |
Source code
|
| .phred2ascii_char |
Source code
|
| .phred2ascii_int |
Source code
|
| .pileup |
Source code
|
| .pileupWhat |
Source code
|
| .pkgLd |
Source code
|
| .pkgMk |
Source code
|
| .ppath |
Source code
|
| .preprocess_bins |
Source code
|
| .printDetailedSummary |
Source code
|
| .printMainSummary |
Source code
|
| .printSummaryHeader |
Source code
|
| .printSummaryLine |
Source code
|
| .readPileup_SNP |
Source code
|
| .readPileup_indel |
Source code
|
| .readPileup_indel_idx |
Source code
|
| .readPileup_table |
Source code
|
| .runlen |
Source code
|
| .scanBamTemplate |
Source code
|
| .scanBam_extract_which_labels |
Source code
|
| .scanBam_postprocess |
Source code
|
| .scanBam_template |
Source code
|
| .scanFa |
Source code
|
| .seqnamesTabix |
Source code
|
| .show_classname |
Source code
|
| .tabix_scan |
Source code
|
| .uunlist |
Source code
|
| .zip |
Source code
|
| ApplyPileupsParam |
Man page
Source code
|
| ApplyPileupsParam-class |
Man page
|
| BamFile |
Man page
Source code
|
| BamFile-class |
Man page
|
| BamFileList |
Man page
Source code
|
| BamFileList-class |
Man page
|
| BamSampler |
Man page
|
| BamSampler-class |
Man page
|
| BamViews |
Man page
|
| BamViews,GRanges-method |
Man page
|
| BamViews,missing-method |
Man page
|
| BamViews-class |
Man page
|
| BcfFile |
Man page
Source code
|
| BcfFile-class |
Man page
|
| BcfFileList |
Man page
Source code
|
| BcfFileList-class |
Man page
|
| FLAG_BITNAMES |
Man page
|
| FaFile |
Man page
Source code
|
| FaFile-class |
Man page
|
| FaFileList |
Man page
Source code
|
| FaFileList-class |
Man page
|
| PileupFiles |
Man page
Source code
|
| PileupFiles,character-method |
Man page
|
| PileupFiles,list-method |
Man page
|
| PileupFiles-class |
Man page
|
| PileupParam |
Man page
Source code
|
| PileupParam-class |
Man page
|
| Rsamtools |
Man page
|
| Rsamtools-package |
Man page
|
| RsamtoolsFile |
Man page
|
| RsamtoolsFile-class |
Man page
|
| RsamtoolsFileList |
Man page
|
| RsamtoolsFileList-class |
Man page
|
| ScanBVcfParam-class |
Man page
|
| ScanBamParam |
Man page
|
| ScanBamParam,ANY-method |
Man page
|
| ScanBamParam,GRanges-method |
Man page
|
| ScanBamParam,IntegerRangesList-method |
Man page
|
| ScanBamParam,missing-method |
Man page
|
| ScanBamParam-class |
Man page
|
| ScanBcfParam |
Man page
|
| ScanBcfParam,GRanges-method |
Man page
|
| ScanBcfParam,GRangesList-method |
Man page
|
| ScanBcfParam,IntegerRangesList-method |
Man page
|
| ScanBcfParam,missing-method |
Man page
|
| ScanBcfParam-class |
Man page
|
| TabixFile |
Man page
Source code
|
| TabixFile-class |
Man page
|
| TabixFileList |
Man page
Source code
|
| TabixFileList-class |
Man page
|
| [,BamViews,ANY,ANY-method |
Man page
|
| [,BamViews,ANY,missing-method |
Man page
Man page
|
| [,BamViews,missing,ANY-method |
Man page
|
| `bamDirname<-` |
Source code
|
| `bamRanges<-` |
Source code
|
| `bamSamples<-` |
Source code
|
| applyPileups |
Man page
|
| applyPileups,PileupFiles,ApplyPileupsParam-method |
Man page
|
| applyPileups,PileupFiles,missing-method |
Man page
|
| asBam |
Man page
|
| asBam,character-method |
Man page
|
| asBcf |
Man page
|
| asBcf,character-method |
Man page
|
| asMates |
Man page
|
| asMates,BamFile-method |
Man page
|
| asMates,BamFileList-method |
Man page
|
| asMates<- |
Man page
|
| asMates<-,BamFile-method |
Man page
|
| asMates<-,BamFileList-method |
Man page
|
| asSam |
Man page
|
| asSam,character-method |
Man page
|
| bamDirname<- |
Man page
|
| bamExperiment |
Man page
Source code
|
| bamFlag |
Man page
Source code
|
| bamFlag<- |
Man page
|
| bamFlagAND |
Man page
Source code
|
| bamFlagAsBitMatrix |
Man page
Source code
|
| bamFlagTest |
Man page
Source code
|
| bamIndicies |
Man page
Source code
|
| bamMapqFilter |
Man page
Source code
|
| bamMapqFilter<- |
Man page
|
| bamPaths |
Man page
Source code
|
| bamRanges |
Man page
Source code
|
| bamRanges<- |
Man page
|
| bamReverseComplement |
Man page
Source code
|
| bamReverseComplement<- |
Man page
|
| bamSamples |
Man page
Source code
|
| bamSamples<- |
Man page
|
| bamSimpleCigar |
Man page
Source code
|
| bamSimpleCigar<- |
Man page
|
| bamTag |
Man page
Source code
|
| bamTag<- |
Man page
|
| bamTagFilter |
Man page
Source code
|
| bamTagFilter<- |
Man page
|
| bamWhat |
Man page
Source code
|
| bamWhat<- |
Man page
|
| bamWhich |
Man page
Source code
|
| bamWhich<- |
Man page
|
| bamWhich<-,ScanBamParam,ANY-method |
Man page
|
| bamWhich<-,ScanBamParam,GRanges-method |
Man page
|
| bamWhich<-,ScanBamParam,IntegerRangesList-method |
Man page
|
| bcfFixed |
Man page
Source code
|
| bcfGeno |
Man page
Source code
|
| bcfInfo |
Man page
Source code
|
| bcfMode |
Man page
Source code
|
| bcfSamples |
Man page
Source code
|
| bcfTrimEmpty |
Man page
Source code
|
| bcfWhich |
Man page
Source code
|
| bgzip |
Man page
Source code
|
| bgzipTabix |
Man page
Source code
|
| bzfile-class |
Man page
|
| close.BamFile |
Man page
Source code
|
| close.BcfFile |
Man page
Source code
|
| close.FaFile |
Man page
Source code
|
| close.RsamtoolsFileList |
Man page
Source code
|
| close.TabixFile |
Man page
Source code
|
| countBam |
Man page
|
| countBam,BamFile-method |
Man page
|
| countBam,BamFileList-method |
Man page
|
| countBam,BamViews-method |
Man page
|
| countBam,character-method |
Man page
|
| countFa |
Man page
|
| countFa,FaFile-method |
Man page
|
| countFa,character-method |
Man page
|
| countTabix |
Man page
Source code
|
| cycle_bins |
Man page
|
| dim,BamViews-method |
Man page
|
| dimnames,BamViews-method |
Man page
|
| dimnames<-,BamViews,ANY-method |
Man page
|
| dimnames<-,BamViews-method |
Man page
|
| distinguish_nucleotides |
Man page
|
| distinguish_strands |
Man page
|
| fifo-class |
Man page
|
| filterBam |
Man page
|
| filterBam,BamFile-method |
Man page
|
| filterBam,character-method |
Man page
|
| getSeq,FaFile-method |
Man page
|
| getSeq,FaFileList-method |
Man page
|
| gzfile-class |
Man page
|
| gzindex |
Man page
|
| gzindex,FaFile-method |
Man page
|
| gzindex,FaFileList-method |
Man page
|
| gzindex<- |
Man page
|
| gzindex<-,FaFile-method |
Man page
|
| gzindex<-,FaFileList-method |
Man page
|
| hasUnmappedMate |
Man page
|
| headerTabix |
Man page
|
| headerTabix,TabixFile-method |
Man page
|
| headerTabix,character-method |
Man page
|
| idxstatsBam |
Man page
|
| idxstatsBam,BamFile-method |
Man page
|
| idxstatsBam,character-method |
Man page
|
| ignore_query_Ns |
Man page
|
| include_deletions |
Man page
|
| include_insertions |
Man page
|
| index |
Man page
|
| index,RsamtoolsFile-method |
Man page
|
| index,RsamtoolsFileList-method |
Man page
|
| index<- |
Man page
|
| index<-,RsamtoolsFile-method |
Man page
|
| index<-,RsamtoolsFileList-method |
Man page
|
| indexBam |
Man page
|
| indexBam,BamFile-method |
Man page
|
| indexBam,character-method |
Man page
|
| indexBcf |
Man page
|
| indexBcf,BcfFile-method |
Man page
|
| indexBcf,character-method |
Man page
|
| indexFa |
Man page
|
| indexFa,FaFile-method |
Man page
|
| indexFa,character-method |
Man page
|
| indexTabix |
Man page
Source code
|
| isDuplicate |
Man page
|
| isFirstMateRead |
Man page
|
| isIncomplete,BamFile-method |
Man page
|
| isMateMinusStrand |
Man page
|
| isMinusStrand |
Man page
|
| isNotPassingQualityControls |
Man page
|
| isNotPrimaryRead |
Man page
|
| isOpen,BamFile-method |
Man page
|
| isOpen,BcfFile-method |
Man page
|
| isOpen,FaFile-method |
Man page
|
| isOpen,PileupFiles-method |
Man page
|
| isOpen,RsamtoolsFile-method |
Man page
|
| isOpen,RsamtoolsFileList-method |
Man page
|
| isOpen,TabixFile-method |
Man page
|
| isPaired |
Man page
|
| isProperPair |
Man page
|
| isSecondMateRead |
Man page
|
| isSecondaryAlignment |
Man page
|
| isUnmappedQuery |
Man page
|
| left_bins |
Man page
|
| max_depth |
Man page
|
| mergeBam |
Man page
|
| mergeBam,BamFileList-method |
Man page
|
| mergeBam,character-method |
Man page
|
| min_base_quality |
Man page
|
| min_mapq |
Man page
|
| min_minor_allele_depth |
Man page
|
| min_nucleotide_depth |
Man page
|
| names,BamViews-method |
Man page
|
| names,RsamtoolsFileList-method |
Man page
|
| names<-,BamViews-method |
Man page
|
| obeyQname |
Man page
|
| obeyQname,BamFile-method |
Man page
|
| obeyQname,BamFileList-method |
Man page
|
| obeyQname<- |
Man page
|
| obeyQname<-,BamFile-method |
Man page
|
| obeyQname<-,BamFileList-method |
Man page
|
| open.BamFile |
Man page
Source code
|
| open.BcfFile |
Man page
Source code
|
| open.FaFile |
Man page
Source code
|
| open.RsamtoolsFileList |
Man page
Source code
|
| open.TabixFile |
Man page
Source code
|
| path |
Man page
|
| path,RsamtoolsFile-method |
Man page
|
| path,RsamtoolsFileList-method |
Man page
|
| phred2ASCIIOffset |
Man page
Source code
|
| pileup |
Man page
|
| pileup,BamFile-method |
Man page
|
| pileup,character-method |
Man page
|
| pipe-class |
Man page
|
| plpFiles |
Man page
Source code
|
| plpFlag |
Man page
Source code
|
| plpFlag<- |
Man page
|
| plpMaxDepth |
Man page
Source code
|
| plpMaxDepth<- |
Man page
|
| plpMinBaseQuality |
Man page
Source code
|
| plpMinBaseQuality<- |
Man page
|
| plpMinDepth |
Man page
Source code
|
| plpMinDepth<- |
Man page
|
| plpMinMapQuality |
Man page
Source code
|
| plpMinMapQuality<- |
Man page
|
| plpParam |
Man page
Source code
|
| plpWhat |
Man page
Source code
|
| plpWhat<- |
Man page
|
| plpWhich |
Man page
Source code
|
| plpWhich<- |
Man page
|
| plpYieldAll |
Man page
Source code
|
| plpYieldAll<- |
Man page
|
| plpYieldBy |
Man page
Source code
|
| plpYieldBy<- |
Man page
|
| plpYieldSize |
Man page
Source code
|
| plpYieldSize<- |
Man page
|
| qnamePrefixEnd |
Man page
|
| qnamePrefixEnd,BamFile-method |
Man page
|
| qnamePrefixEnd,BamFileList-method |
Man page
|
| qnamePrefixEnd<- |
Man page
|
| qnamePrefixEnd<-,BamFile-method |
Man page
|
| qnamePrefixEnd<-,BamFileList-method |
Man page
|
| qnameSuffixStart |
Man page
|
| qnameSuffixStart,BamFile-method |
Man page
|
| qnameSuffixStart,BamFileList-method |
Man page
|
| qnameSuffixStart<- |
Man page
|
| qnameSuffixStart<-,BamFile-method |
Man page
|
| qnameSuffixStart<-,BamFileList-method |
Man page
|
| query_bins |
Man page
|
| quickBamCounts |
Man page
Source code
|
| quickBamFlagSummary |
Man page
|
| quickBamFlagSummary,BamFile-method |
Man page
|
| quickBamFlagSummary,character-method |
Man page
|
| quickBamFlagSummary,list-method |
Man page
|
| quickCountBam |
Man page
Source code
|
| razip |
Man page
Source code
|
| readPileup |
Man page
|
| readPileup,character-method |
Man page
|
| readPileup,connection-method |
Man page
|
| scanBam |
Man page
|
| scanBam,BamFile-method |
Man page
|
| scanBam,BamSampler-method |
Man page
|
| scanBam,BamViews-method |
Man page
|
| scanBam,character-method |
Man page
|
| scanBamFlag |
Man page
Source code
|
| scanBamHeader |
Man page
|
| scanBamHeader,BamFile-method |
Man page
|
| scanBamHeader,character-method |
Man page
|
| scanBamWhat |
Man page
Source code
|
| scanBcf |
Man page
|
| scanBcf,BcfFile-method |
Man page
|
| scanBcf,character-method |
Man page
|
| scanBcfHeader |
Man page
|
| scanBcfHeader,BcfFile-method |
Man page
|
| scanBcfHeader,character-method |
Man page
|
| scanFa |
Man page
|
| scanFa,FaFile,GRanges-method |
Man page
|
| scanFa,FaFile,IntegerRangesList-method |
Man page
|
| scanFa,FaFile,missing-method |
Man page
|
| scanFa,character,GRanges-method |
Man page
|
| scanFa,character,IntegerRangesList-method |
Man page
|
| scanFa,character,missing-method |
Man page
|
| scanFaIndex |
Man page
|
| scanFaIndex,FaFile-method |
Man page
|
| scanFaIndex,FaFileList-method |
Man page
|
| scanFaIndex,character-method |
Man page
|
| scanTabix |
Man page
|
| scanTabix,TabixFile,GRanges-method |
Man page
|
| scanTabix,TabixFile,IntegerRangesList-method |
Man page
|
| scanTabix,TabixFile,missing-method |
Man page
|
| scanTabix,character,ANY-method |
Man page
|
| scanTabix,character,GRanges-method |
Man page
|
| scanTabix,character,IntegerRangesList-method |
Man page
|
| scanTabix,character,missing-method |
Man page
|
| seqinfo,BamFile-method |
Man page
|
| seqinfo,BamFileList-method |
Man page
|
| seqinfo,FaFile-method |
Man page
|
| seqnamesTabix |
Man page
|
| seqnamesTabix,TabixFile-method |
Man page
|
| seqnamesTabix,character-method |
Man page
|
| show,ApplyPileupsParam-method |
Man page
|
| show,BamFile-method |
Man page
|
| show,BamFileList-method |
Man page
|
| show,BamSampler-method |
Man page
|
| show,BamViews-method |
Man page
|
| show,FaFile-method |
Man page
|
| show,PileupFiles-method |
Man page
|
| show,PileupParam-method |
Man page
|
| show,RsamtoolsFile-method |
Man page
|
| show,ScanBVcfParam-method |
Man page
|
| show,ScanBamParam-method |
Man page
|
| sortBam |
Man page
|
| sortBam,BamFile-method |
Man page
|
| sortBam,character-method |
Man page
|
| testPairedEndBam |
Man page
|
| testPairedEndBam,BamFile-method |
Man page
|
| testPairedEndBam,character-method |
Man page
|
| unz-class |
Man page
|
| url-class |
Man page
|
| yieldBam |
Man page
|
| yieldSize |
Man page
|
| yieldSize,RsamtoolsFile-method |
Man page
|
| yieldSize,RsamtoolsFileList-method |
Man page
|
| yieldSize<- |
Man page
|
| yieldSize<-,RsamtoolsFile-method |
Man page
|
| yieldSize<-,RsamtoolsFileList-method |
Man page
|
| yieldTabix |
Man page
|
| yieldTabix,TabixFile-method |
Man page
|
