GenomicAlignments: Representation and manipulation of short genomic alignments

Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

AuthorHervé Pagès, Valerie Obenchain, Martin Morgan
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.10.1

View on Bioconductor

Functions

alphabetFrequencyFromBam Man page
as.data.frame,GAlignments-method Man page
as.data.frame.OverlapEncodings Man page
as.data.frame,OverlapEncodings-method Man page
c,GAlignmentPairs-method Man page
c,GAlignmentsList-method Man page
c,GAlignments-method Man page
c,GappedReads-method Man page
cigar Man page
cigar,GAlignmentsList-method Man page
cigar,GAlignments-method Man page
cigarNarrow Man page
CIGAR_OPS Man page
cigarOpTable Man page
cigarQNarrow Man page
cigarRangesAlongPairwiseSpace Man page
cigarRangesAlongQuerySpace Man page
cigarRangesAlongReferenceSpace Man page
cigarToRleList Man page
cigar-utils Man page
cigarWidthAlongPairwiseSpace Man page
cigarWidthAlongQuerySpace Man page
cigarWidthAlongReferenceSpace Man page
class:GAlignmentPairs Man page
class:GAlignments Man page
class:GAlignmentsList Man page
class:GappedReads Man page
class:OverlapEncodings Man page
coerce,GAlignmentPairs,GAlignmentsList-method Man page
coerce,GAlignmentPairs,GAlignments-method Man page
coerce,GAlignmentPairs,GRangesList-method Man page
coerce,GAlignmentPairs,GRanges-method Man page
coerce,GAlignmentPairs,Ranges-method Man page
coerce,GAlignments,GRangesList-method Man page
coerce,GAlignments,GRanges-method Man page
coerce,GAlignmentsList,GRangesList-method Man page
coerce,GAlignmentsList,GRanges-method Man page
coerce,GAlignmentsList,RangesList-method Man page
coerce,GAlignmentsList,Ranges-method Man page
coerce,GAlignments,RangesList-method Man page
coerce,GAlignments,Ranges-method Man page
coerce,GenomicRanges,GAlignments-method Man page
coordinate-mapping-methods Man page
countCompatibleOverlaps Man page
countDumpedAlignments Man page
coverage Man page
coverage,BamFile-method Man page
coverage,character-method Man page
coverage,GAlignmentPairs-method Man page
coverage,GAlignmentsList-method Man page
coverage,GAlignments-method Man page
coverage-methods Man page
elementMetadata<-,GAlignmentsList-method Man page
elementMetadata,GAlignmentsList-method Man page
encodeOverlaps Man page
encodeOverlaps1 Man page
encodeOverlaps,GRangesList,GRangesList-method Man page
encodeOverlaps-methods Man page
encodeOverlaps,RangesList,RangesList-method Man page
encodeOverlaps,RangesList,Ranges-method Man page
encodeOverlaps,Ranges,RangesList-method Man page
encoding,OverlapEncodings-method Man page
end,GAlignmentsList-method Man page
end,GAlignments-method Man page
explodeCigarOpLengths Man page
explodeCigarOps Man page
extractAlignmentRangesOnReference Man page
extractQueryStartInTranscript Man page
extractSkippedExonRanks Man page
extractSkippedExonRanks,character-method Man page
extractSkippedExonRanks,factor-method Man page
extractSkippedExonRanks,OverlapEncodings-method Man page
extractSpannedExonRanks Man page
extractSpannedExonRanks,character-method Man page
extractSpannedExonRanks,factor-method Man page
extractSpannedExonRanks,OverlapEncodings-method Man page
extractSteppedExonRanks Man page
extractSteppedExonRanks,character-method Man page
extractSteppedExonRanks,factor-method Man page
extractSteppedExonRanks,OverlapEncodings-method Man page
findCompatibleOverlaps Man page
findCompatibleOverlaps,GAlignmentPairs,GRangesList-method Man page
findCompatibleOverlaps,GAlignments,GRangesList-method Man page
findCompatibleOverlaps-methods Man page
findMateAlignment Man page
findMateAlignment2 Man page
findOverlaps Man page
findOverlaps,GAlignmentPairs,GAlignmentPairs-method Man page
findOverlaps,GAlignmentPairs,Vector-method Man page
findOverlaps,GAlignments,GAlignments-method Man page
findOverlaps,GAlignmentsList,GAlignmentsList-method Man page
findOverlaps,GAlignmentsList,Vector-method Man page
findOverlaps,GAlignments,Vector-method Man page
findOverlaps-methods Man page
findOverlaps,Vector,GAlignmentPairs-method Man page
findOverlaps,Vector,GAlignmentsList-method Man page
findOverlaps,Vector,GAlignments-method Man page
findSpliceOverlaps Man page
findSpliceOverlaps,BamFile,ANY-method Man page
findSpliceOverlaps,character,ANY-method Man page
findSpliceOverlaps,GAlignmentPairs,GRangesList-method Man page
findSpliceOverlaps,GAlignments,GRangesList-method Man page
findSpliceOverlaps,GRangesList,GRangesList-method Man page
findSpliceOverlaps-methods Man page
first Man page
first,GAlignmentPairs-method Man page
flippedQuery Man page
flippedQuery,OverlapEncodings-method Man page
flipQuery Man page
flushDumpedAlignments Man page
GAlignmentPairs Man page
[[,GAlignmentPairs,ANY,ANY-method Man page
GAlignmentPairs-class Man page
GAlignments Man page
GAlignments-class Man page
GAlignmentsList Man page
GAlignmentsList Man page
GAlignmentsList-class Man page
GappedReads Man page
GappedReads-class Man page
getDumpedAlignments Man page
granges,GAlignmentPairs-method Man page
granges,GAlignmentsList-method Man page
granges,GAlignments-method Man page
grglist,GAlignmentPairs-method Man page
grglist,GAlignmentsList-method Man page
grglist,GAlignments-method Man page
IntersectionNotEmpty Man page
IntersectionStrict Man page
intra-range-methods Man page
invertStrand,GAlignmentPairs-method Man page
isCompatibleWithSkippedExons Man page
isCompatibleWithSkippedExons,character-method Man page
isCompatibleWithSkippedExons,factor-method Man page
isCompatibleWithSkippedExons,OverlapEncodings-method Man page
isCompatibleWithSplicing Man page
isCompatibleWithSplicing,character-method Man page
isCompatibleWithSplicing,factor-method Man page
isCompatibleWithSplicing,OverlapEncodings-method Man page
isProperPair Man page
isProperPair,GAlignmentPairs-method Man page
junctions Man page
junctions,GAlignmentPairs-method Man page
junctions,GAlignmentsList-method Man page
junctions,GAlignments-method Man page
junctions-methods Man page
last Man page
last,GAlignmentPairs-method Man page
Lencoding Man page
Lencoding,character-method Man page
Lencoding,factor-method Man page
Lencoding,OverlapEncodings-method Man page
length,GAlignmentPairs-method Man page
length,GAlignments-method Man page
length,OverlapEncodings-method Man page
levels.OverlapEncodings Man page
levels,OverlapEncodings-method Man page
Lnjunc Man page
Lnjunc,character-method Man page
Lnjunc,factor-method Man page
Lnjunc,OverlapEncodings-method Man page
Loffset Man page
Loffset,OverlapEncodings-method Man page
makeGAlignmentPairs Man page
mapFromAlignments Man page
mapFromAlignments,GenomicRanges,GAlignments-method Man page
mapFromAlignments,Ranges,GAlignments-method Man page
mapToAlignments Man page
mapToAlignments,GenomicRanges,GAlignments-method Man page
mapToAlignments,Ranges,GAlignments-method Man page
names<-,GAlignmentPairs-method Man page
names,GAlignmentPairs-method Man page
names<-,GAlignmentsList-method Man page
names,GAlignmentsList-method Man page
names<-,GAlignments-method Man page
names,GAlignments-method Man page
narrow Man page
narrow,GAlignmentsList-method Man page
narrow,GAlignments-method Man page
narrow,GappedReads-method Man page
NATURAL_INTRON_MOTIFS Man page
njunc Man page
njunc,character-method Man page
njunc,factor-method Man page
njunc,GAlignmentPairs-method Man page
njunc,GAlignmentsList-method Man page
njunc,GAlignments-method Man page
njunc,OverlapEncodings-method Man page
OverlapEncodings Man page
OverlapEncodings-class Man page
pileLettersAt Man page
pintersect Man page
pintersect,GAlignments,GRanges-method Man page
pintersect,GRanges,GAlignments-method Man page
pmapFromAlignments Man page
pmapFromAlignments,GenomicRanges,GAlignments-method Man page
pmapFromAlignments,Ranges,GAlignments-method Man page
pmapToAlignments Man page
pmapToAlignments,GenomicRanges,GAlignments-method Man page
pmapToAlignments,Ranges,GAlignments-method Man page
qnarrow Man page
qnarrow,GAlignmentsList-method Man page
qnarrow,GAlignments-method Man page
qnarrow,GappedReads-method Man page
qseq Man page
qseq,GappedReads-method Man page
queryLoc2refLoc Man page
queryLocs2refLocs Man page
qwidth Man page
qwidth,GAlignmentsList-method Man page
qwidth,GAlignments-method Man page
qwidth,GappedReads-method Man page
ranges,GAlignmentPairs-method Man page
ranges,GAlignmentsList-method Man page
ranges,GAlignments-method Man page
readGAlignmentPairs Man page
readGAlignmentPairs,BamFile-method Man page
readGAlignmentPairs,character-method Man page
readGAlignments Man page
readGAlignments,BamFile-method Man page
readGAlignments,BamViews-method Man page
readGAlignments,character-method Man page
readGAlignmentsList Man page
readGAlignmentsList,BamFile-method Man page
readGAlignmentsList,character-method Man page
readGappedReads Man page
readGappedReads,BamFile-method Man page
readGappedReads,character-method Man page
readSTARJunctions Man page
readTopHatJunctions Man page
relistToClass,GAlignments-method Man page
Rencoding Man page
Rencoding,character-method Man page
Rencoding,factor-method Man page
Rencoding,OverlapEncodings-method Man page
rglist,GAlignmentsList-method Man page
rglist,GAlignments-method Man page
rname Man page
rname<- Man page
rname<-,GAlignmentsList-method Man page
rname,GAlignmentsList-method Man page
rname<-,GAlignments-method Man page
rname,GAlignments-method Man page
Rnjunc Man page
Rnjunc,character-method Man page
Rnjunc,factor-method Man page
Rnjunc,OverlapEncodings-method Man page
Roffset Man page
Roffset,OverlapEncodings-method Man page
second Man page
second,GAlignmentPairs-method Man page
selectEncodingWithCompatibleStrand Man page
seqinfo<-,GAlignmentPairs-method Man page
seqinfo,GAlignmentPairs-method Man page
seqinfo<-,GAlignmentsList-method Man page
seqinfo,GAlignmentsList-method Man page
seqinfo<-,GAlignments-method Man page
seqinfo,GAlignments-method Man page
seqlevelsInUse,GAlignmentPairs-method Man page
seqnames,GAlignmentPairs-method Man page
seqnames<-,GAlignmentsList-method Man page
seqnames,GAlignmentsList-method Man page
seqnames<-,GAlignments-method Man page
seqnames,GAlignments-method Man page
sequenceLayer Man page
setops-methods Man page
show,GAlignmentPairs-method Man page
show,GAlignmentsList-method Man page
show,GAlignments-method Man page
show,OverlapEncodings-method Man page
stackStringsFromBam Man page
start,GAlignmentsList-method Man page
start,GAlignments-method Man page
strand,GAlignmentPairs-method Man page
strand<-,GAlignmentsList,character-method Man page
strand<-,GAlignmentsList-method Man page
strand,GAlignmentsList-method Man page
strand<-,GAlignments-method Man page
strand,GAlignments-method Man page
strandMode Man page
strandMode<- Man page
strandMode<-,GAlignmentPairs-method Man page
strandMode,GAlignmentPairs-method Man page
summarizeJunctions Man page
summarizeOverlaps Man page
summarizeOverlaps,BamViews,missing-method Man page
summarizeOverlaps,GRanges,BamFileList-method Man page
summarizeOverlaps,GRanges,BamFile-method Man page
summarizeOverlaps,GRanges,character-method Man page
summarizeOverlaps,GRanges,GAlignmentPairs-method Man page
summarizeOverlaps,GRanges,GAlignmentsList-method Man page
summarizeOverlaps,GRanges,GAlignments-method Man page
summarizeOverlaps,GRanges,GRangesList-method Man page
summarizeOverlaps,GRanges,GRanges-method Man page
summarizeOverlaps,GRangesList,BamFileList-method Man page
summarizeOverlaps,GRangesList,BamFile-method Man page
summarizeOverlaps,GRangesList,character-method Man page
summarizeOverlaps,GRangesList,GAlignmentPairs-method Man page
summarizeOverlaps,GRangesList,GAlignmentsList-method Man page
summarizeOverlaps,GRangesList,GAlignments-method Man page
summarizeOverlaps,GRangesList,GRangesList-method Man page
summarizeOverlaps,GRangesList,GRanges-method Man page
summarizeOverlaps-methods Man page
Union Man page
unlist,GAlignmentPairs-method Man page
updateObject,GAlignmentsList-method Man page
updateObject,GAlignments-method Man page
validCigar Man page
width,GAlignmentsList-method Man page
width,GAlignments-method Man page

Files

GenomicAlignments/DESCRIPTION
GenomicAlignments/NAMESPACE
GenomicAlignments/NEWS
GenomicAlignments/R
GenomicAlignments/R/GAlignmentPairs-class.R GenomicAlignments/R/GAlignments-class.R GenomicAlignments/R/GAlignmentsList-class.R GenomicAlignments/R/GappedReads-class.R GenomicAlignments/R/OverlapEncodings-class.R GenomicAlignments/R/cigar-utils.R GenomicAlignments/R/coordinate-mapping-methods.R GenomicAlignments/R/coverage-methods.R GenomicAlignments/R/encodeOverlaps-methods.R GenomicAlignments/R/findCompatibleOverlaps-methods.R GenomicAlignments/R/findMateAlignment.R GenomicAlignments/R/findOverlaps-methods.R GenomicAlignments/R/findSpliceOverlaps-methods.R GenomicAlignments/R/intra-range-methods.R GenomicAlignments/R/junctions-methods.R GenomicAlignments/R/pileLettersAt.R GenomicAlignments/R/readGAlignments.R GenomicAlignments/R/sequenceLayer.R GenomicAlignments/R/setops-methods.R GenomicAlignments/R/stackStringsFromBam.R GenomicAlignments/R/summarizeOverlaps-methods.R GenomicAlignments/R/zzz.R
GenomicAlignments/build
GenomicAlignments/build/vignette.rds
GenomicAlignments/inst
GenomicAlignments/inst/CITATION
GenomicAlignments/inst/doc
GenomicAlignments/inst/doc/GenomicAlignmentsIntroduction.R
GenomicAlignments/inst/doc/GenomicAlignmentsIntroduction.Rnw
GenomicAlignments/inst/doc/GenomicAlignmentsIntroduction.pdf
GenomicAlignments/inst/doc/OverlapEncodings.R
GenomicAlignments/inst/doc/OverlapEncodings.Rnw
GenomicAlignments/inst/doc/OverlapEncodings.pdf
GenomicAlignments/inst/doc/WorkingWithAlignedNucleotides.R
GenomicAlignments/inst/doc/WorkingWithAlignedNucleotides.Rnw
GenomicAlignments/inst/doc/WorkingWithAlignedNucleotides.pdf
GenomicAlignments/inst/doc/summarizeOverlaps.R
GenomicAlignments/inst/doc/summarizeOverlaps.Rnw
GenomicAlignments/inst/doc/summarizeOverlaps.pdf
GenomicAlignments/inst/extdata
GenomicAlignments/inst/extdata/sm_treated1.bam
GenomicAlignments/inst/extdata/sm_untreated1.bam
GenomicAlignments/inst/unitTests
GenomicAlignments/inst/unitTests/test_GAlignments-class.R
GenomicAlignments/inst/unitTests/test_GAlignmentsList-class.R
GenomicAlignments/inst/unitTests/test_cigar-utils.R
GenomicAlignments/inst/unitTests/test_coordinate-mapping-methods.R
GenomicAlignments/inst/unitTests/test_findSpliceOverlaps-methods.R
GenomicAlignments/inst/unitTests/test_intra-range-methods.R
GenomicAlignments/inst/unitTests/test_readGAlignmentPairs.R
GenomicAlignments/inst/unitTests/test_readGAlignments.R
GenomicAlignments/inst/unitTests/test_readGAlignmentsList.R
GenomicAlignments/inst/unitTests/test_summarizeOverlaps-methods.R
GenomicAlignments/man
GenomicAlignments/man/GAlignmentPairs-class.Rd GenomicAlignments/man/GAlignments-class.Rd GenomicAlignments/man/GAlignmentsList-class.Rd GenomicAlignments/man/GappedReads-class.Rd GenomicAlignments/man/OverlapEncodings-class.Rd GenomicAlignments/man/cigar-utils.Rd GenomicAlignments/man/coordinate-mapping-methods.Rd GenomicAlignments/man/coverage-methods.Rd GenomicAlignments/man/encodeOverlaps-methods.Rd GenomicAlignments/man/findCompatibleOverlaps-methods.Rd GenomicAlignments/man/findMateAlignment.Rd GenomicAlignments/man/findOverlaps-methods.Rd GenomicAlignments/man/findSpliceOverlaps-methods.Rd GenomicAlignments/man/intra-range-methods.Rd GenomicAlignments/man/junctions-methods.Rd GenomicAlignments/man/pileLettersAt.Rd GenomicAlignments/man/readGAlignments.Rd GenomicAlignments/man/sequenceLayer.Rd GenomicAlignments/man/setops-methods.Rd GenomicAlignments/man/stackStringsFromBam.Rd GenomicAlignments/man/summarizeOverlaps-methods.Rd
GenomicAlignments/src
GenomicAlignments/src/GenomicAlignments.h
GenomicAlignments/src/IRanges_stubs.c
GenomicAlignments/src/R_init_GenomicAlignments.c
GenomicAlignments/src/S4Vectors_stubs.c
GenomicAlignments/src/cigar_utils.c
GenomicAlignments/src/coordinate_mapping_methods.c
GenomicAlignments/src/encodeOverlaps_methods.c
GenomicAlignments/tests
GenomicAlignments/tests/run_unitTests.R
GenomicAlignments/vignettes
GenomicAlignments/vignettes/GenomicAlignmentsIntroduction.Rnw
GenomicAlignments/vignettes/OverlapEncodings.Rnw
GenomicAlignments/vignettes/WorkingWithAlignedNucleotides.Rnw
GenomicAlignments/vignettes/precomputed_results
GenomicAlignments/vignettes/precomputed_results/U1.sbcompHITSa.rda
GenomicAlignments/vignettes/precomputed_results/U1.sbcompHITSb.rda
GenomicAlignments/vignettes/precomputed_results/exbytx.rda
GenomicAlignments/vignettes/summarizeOverlaps-modes.pdf
GenomicAlignments/vignettes/summarizeOverlaps.Rnw

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