# Representation and manipulation of short genomic alignments

## Documentation for package ‘GenomicAlignments’ version 1.22.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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 --

parallelSlotNames-method | GAlignmentPairs objects
parallelSlotNames-method | GAlignments objects
parallelSlotNames-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 | 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