Representation and manipulation of short genomic alignments
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘GenomicAlignments’ version 1.40.0
Help Pages
A B C E F G I J L M N O P Q R S U V W misc
-- A --
| alphabetFrequencyFromBam | Stack the read sequences stored in a GAlignments object or a BAM file |
| as.data.frame-method | GAlignmentPairs objects |
| as.data.frame-method | GAlignments objects |
| as.data.frame-method | OverlapEncodings objects |
| as.data.frame.OverlapEncodings | OverlapEncodings objects |
-- B --
| bindROWS-method | GAlignmentPairs objects |
| bindROWS-method | GAlignments objects |
-- C --
| c-method | (Legacy) GappedReads objects |
| cigar | GAlignments objects |
| cigar-method | GAlignments objects |
| cigar-method | GAlignmentsList objects |
| cigar-utils | CIGAR utility functions |
| cigarNarrow | CIGAR utility functions |
| cigarOpTable | CIGAR utility functions |
| cigarQNarrow | CIGAR utility functions |
| cigarRangesAlongPairwiseSpace | CIGAR utility functions |
| cigarRangesAlongQuerySpace | CIGAR utility functions |
| cigarRangesAlongReferenceSpace | CIGAR utility functions |
| cigarToRleList | CIGAR utility functions |
| cigarWidthAlongPairwiseSpace | CIGAR utility functions |
| cigarWidthAlongQuerySpace | CIGAR utility functions |
| cigarWidthAlongReferenceSpace | CIGAR utility functions |
| CIGAR_OPS | CIGAR utility functions |
| class:GAlignmentPairs | GAlignmentPairs objects |
| class:GAlignments | GAlignments objects |
| class:GAlignmentsList | GAlignmentsList objects |
| class:GappedReads | (Legacy) GappedReads objects |
| class:OverlapEncodings | OverlapEncodings objects |
| coerce-method | GAlignmentPairs objects |
| coerce-method | GAlignments objects |
| coerce-method | GAlignmentsList objects |
| coordinate-mapping-methods | Map range coordinates between reads and genome space using CIGAR alignments |
| countCompatibleOverlaps | Finding hits between reads and transcripts that are _compatible_ with the splicing of the transcript |
| countDumpedAlignments | Pairing the elements of a GAlignments object |
| coverage | Coverage of a GAlignments, GAlignmentPairs, or GAlignmentsList object |
| coverage-method | Coverage of a GAlignments, GAlignmentPairs, or GAlignmentsList object |
| coverage-methods | Coverage of a GAlignments, GAlignmentPairs, or GAlignmentsList object |
-- E --
| elementMetadata-method | GAlignmentsList objects |
| elementMetadata<--method | GAlignmentsList objects |
| encodeOverlaps | Encode the overlaps between RNA-seq reads and the transcripts of a gene model |
| encodeOverlaps-method | Encode the overlaps between RNA-seq reads and the transcripts of a gene model |
| encodeOverlaps-methods | Encode the overlaps between RNA-seq reads and the transcripts of a gene model |
| encodeOverlaps1 | Encode the overlaps between RNA-seq reads and the transcripts of a gene model |
| encoding-method | OverlapEncodings objects |
| encodingHalves | OverlapEncodings objects |
| encodingHalves-method | OverlapEncodings objects |
| explodeCigarOpLengths | CIGAR utility functions |
| explodeCigarOps | CIGAR utility functions |
| extractAlignmentRangesOnReference | CIGAR utility functions |
| extractQueryStartInTranscript | Encode the overlaps between RNA-seq reads and the transcripts of a gene model |
| extractSkippedExonRanks | Encode the overlaps between RNA-seq reads and the transcripts of a gene model |
| extractSkippedExonRanks-method | Encode the overlaps between RNA-seq reads and the transcripts of a gene model |
| extractSpannedExonRanks | Encode the overlaps between RNA-seq reads and the transcripts of a gene model |
| extractSpannedExonRanks-method | Encode the overlaps between RNA-seq reads and the transcripts of a gene model |
| extractSteppedExonRanks | Encode the overlaps between RNA-seq reads and the transcripts of a gene model |
| extractSteppedExonRanks-method | Encode the overlaps between RNA-seq reads and the transcripts of a gene model |
-- F --
| findCompatibleOverlaps | Finding hits between reads and transcripts that are _compatible_ with the splicing of the transcript |
| findCompatibleOverlaps-method | Finding hits between reads and transcripts that are _compatible_ with the splicing of the transcript |
| findCompatibleOverlaps-methods | Finding hits between reads and transcripts that are _compatible_ with the splicing of the transcript |
| findMateAlignment | Pairing the elements of a GAlignments object |
| findOverlaps | Finding overlapping genomic alignments |
| findOverlaps-method | Finding overlapping genomic alignments |
| findOverlaps-methods | Finding overlapping genomic alignments |
| findSpliceOverlaps | Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice events |
| findSpliceOverlaps-method | Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice events |
| findSpliceOverlaps-methods | Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice events |
| first | GAlignmentPairs objects |
| first-method | GAlignmentPairs objects |
| flippedQuery | OverlapEncodings objects |
| flippedQuery-method | OverlapEncodings objects |
| flipQuery | Encode the overlaps between RNA-seq reads and the transcripts of a gene model |
| flushDumpedAlignments | Pairing the elements of a GAlignments object |
-- G --
| GAlignmentPairs | GAlignmentPairs objects |
| GAlignmentPairs-class | GAlignmentPairs objects |
| GAlignments | GAlignments objects |
| GAlignments-class | GAlignments objects |
| GAlignmentsList | GAlignmentsList objects |
| GAlignmentsList-class | GAlignmentsList objects |
| GappedReads | (Legacy) GappedReads objects |
| GappedReads-class | (Legacy) GappedReads objects |
| getDumpedAlignments | Pairing the elements of a GAlignments object |
| getListElement-method | GAlignments objects |
| granges-method | GAlignmentPairs objects |
| granges-method | GAlignments objects |
| granges-method | GAlignmentsList objects |
| grglist-method | GAlignmentPairs objects |
| grglist-method | GAlignments objects |
| grglist-method | GAlignmentsList objects |
-- I --
| IntersectionNotEmpty | Perform overlap queries between reads and genomic features |
| IntersectionStrict | Perform overlap queries between reads and genomic features |
| intra-range-methods | Intra range transformations of a GAlignments or GAlignmentsList object |
| invertStrand-method | GAlignmentPairs objects |
| is.unsorted-method | GAlignments objects |
| isCompatibleWithSkippedExons | Encode the overlaps between RNA-seq reads and the transcripts of a gene model |
| isCompatibleWithSkippedExons-method | Encode the overlaps between RNA-seq reads and the transcripts of a gene model |
| isCompatibleWithSplicing | OverlapEncodings objects |
| isCompatibleWithSplicing-method | OverlapEncodings objects |
| isProperPair | GAlignmentPairs objects |
| isProperPair-method | GAlignmentPairs objects |
-- J --
| junctions | Extract junctions from genomic alignments |
| junctions-method | Extract junctions from genomic alignments |
| junctions-methods | Extract junctions from genomic alignments |
-- L --
| last | GAlignmentPairs objects |
| last-method | GAlignmentPairs objects |
| Lencoding | OverlapEncodings objects |
| levels-method | OverlapEncodings objects |
| levels.OverlapEncodings | OverlapEncodings objects |
| Lnjunc | OverlapEncodings objects |
| Loffset | OverlapEncodings objects |
| Loffset-method | OverlapEncodings objects |
-- M --
| makeGAlignmentPairs | Pairing the elements of a GAlignments object |
| mapFromAlignments | Map range coordinates between reads and genome space using CIGAR alignments |
| mapFromAlignments-method | Map range coordinates between reads and genome space using CIGAR alignments |
| mapToAlignments | Map range coordinates between reads and genome space using CIGAR alignments |
| mapToAlignments-method | Map range coordinates between reads and genome space using CIGAR alignments |
-- N --
| names-method | GAlignmentPairs objects |
| names-method | GAlignments objects |
| names-method | GAlignmentsList objects |
| names<--method | GAlignmentPairs objects |
| names<--method | GAlignments objects |
| names<--method | GAlignmentsList objects |
| narrow-method | Intra range transformations of a GAlignments or GAlignmentsList object |
| NATURAL_INTRON_MOTIFS | Extract junctions from genomic alignments |
| njunc | GAlignments objects |
| njunc-method | GAlignmentPairs objects |
| njunc-method | GAlignments objects |
| njunc-method | GAlignmentsList objects |
| njunc-method | OverlapEncodings objects |
-- O --
| order-method | GAlignments objects |
| OverlapEncodings | OverlapEncodings objects |
| OverlapEncodings-class | OverlapEncodings objects |
-- P --
| parallel_slot_names-method | GAlignmentPairs objects |
| parallel_slot_names-method | GAlignments objects |
| parallel_slot_names-method | OverlapEncodings objects |
| pcompare-method | GAlignments objects |
| pileLettersAt | Pile the letters of a set of aligned reads on top of a set of genomic positions |
| pintersect | Set operations on GAlignments objects |
| pintersect-method | Set operations on GAlignments objects |
| pmapFromAlignments | Map range coordinates between reads and genome space using CIGAR alignments |
| pmapFromAlignments-method | Map range coordinates between reads and genome space using CIGAR alignments |
| pmapToAlignments | Map range coordinates between reads and genome space using CIGAR alignments |
| pmapToAlignments-method | Map range coordinates between reads and genome space using CIGAR alignments |
-- Q --
| qnarrow | Intra range transformations of a GAlignments or GAlignmentsList object |
| qnarrow-method | Intra range transformations of a GAlignments or GAlignmentsList object |
| qseq | (Legacy) GappedReads objects |
| qseq-method | (Legacy) GappedReads objects |
| queryLoc2refLoc | CIGAR utility functions |
| queryLocs2refLocs | CIGAR utility functions |
| qwidth | GAlignments objects |
| qwidth-method | GAlignments objects |
| qwidth-method | GAlignmentsList objects |
| qwidth-method | (Legacy) GappedReads objects |
-- R --
| ranges-method | GAlignmentPairs objects |
| ranges-method | GAlignments objects |
| ranges-method | GAlignmentsList objects |
| rank-method | GAlignments objects |
| readGAlignmentPairs | Reading genomic alignments from a file |
| readGAlignmentPairs-method | Reading genomic alignments from a file |
| readGAlignments | Reading genomic alignments from a file |
| readGAlignments-method | Reading genomic alignments from a file |
| readGAlignmentsList | Reading genomic alignments from a file |
| readGAlignmentsList-method | Reading genomic alignments from a file |
| readGappedReads | Reading genomic alignments from a file |
| readGappedReads-method | Reading genomic alignments from a file |
| readSTARJunctions | Extract junctions from genomic alignments |
| readTopHatJunctions | Extract junctions from genomic alignments |
| relistToClass-method | GAlignmentsList objects |
| Rencoding | OverlapEncodings objects |
| rglist-method | GAlignments objects |
| rglist-method | GAlignmentsList objects |
| rname | GAlignments objects |
| rname-method | GAlignments objects |
| rname-method | GAlignmentsList objects |
| rname<- | GAlignments objects |
| rname<--method | GAlignments objects |
| rname<--method | GAlignmentsList objects |
| Rnjunc | OverlapEncodings objects |
| Roffset | OverlapEncodings objects |
| Roffset-method | OverlapEncodings objects |
-- S --
| second | GAlignmentPairs objects |
| second-method | GAlignmentPairs objects |
| selectEncodingWithCompatibleStrand | Encode the overlaps between RNA-seq reads and the transcripts of a gene model |
| seqinfo-method | GAlignmentPairs objects |
| seqinfo-method | GAlignments objects |
| seqinfo-method | GAlignmentsList objects |
| seqinfo<--method | GAlignmentPairs objects |
| seqinfo<--method | GAlignments objects |
| seqinfo<--method | GAlignmentsList objects |
| seqlevelsInUse-method | GAlignmentPairs objects |
| seqnames-method | GAlignmentPairs objects |
| seqnames-method | GAlignments objects |
| seqnames-method | GAlignmentsList objects |
| seqnames<--method | GAlignments objects |
| seqnames<--method | GAlignmentsList objects |
| sequenceLayer | Lay read sequences alongside the reference space, using their CIGARs |
| setops-methods | Set operations on GAlignments objects |
| show-method | GAlignmentPairs objects |
| show-method | GAlignments objects |
| show-method | GAlignmentsList objects |
| show-method | OverlapEncodings objects |
| sort-method | GAlignments objects |
| stackStringsFromBam | Stack the read sequences stored in a GAlignments object or a BAM file |
| stackStringsFromGAlignments | Stack the read sequences stored in a GAlignments object or a BAM file |
| start-method | GAlignments objects |
| strand-method | GAlignmentPairs objects |
| strand-method | GAlignments objects |
| strand-method | GAlignmentsList objects |
| strand<--method | GAlignments objects |
| strand<--method | GAlignmentsList objects |
| strandMode | GAlignmentPairs objects |
| strandMode-method | GAlignmentPairs objects |
| strandMode<- | GAlignmentPairs objects |
| strandMode<--method | GAlignmentPairs objects |
| summarizeJunctions | Extract junctions from genomic alignments |
| summarizeOverlaps | Perform overlap queries between reads and genomic features |
| summarizeOverlaps-method | Perform overlap queries between reads and genomic features |
| summarizeOverlaps-methods | Perform overlap queries between reads and genomic features |
-- U --
| Union | Perform overlap queries between reads and genomic features |
| unlist-method | GAlignmentPairs objects |
| update-method | GAlignments objects |
| updateObject-method | GAlignmentPairs objects |
| updateObject-method | GAlignments objects |
-- V --
| validCigar | CIGAR utility functions |
-- W --
| width-method | GAlignments objects |
| windows-method | Intra range transformations of a GAlignments or GAlignmentsList object |
-- misc --
| [[-method | GAlignmentPairs objects |