GenomicAlignments: Representation and manipulation of short genomic alignments
Version 1.12.1

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
Bioconductor views Alignment Coverage DataImport Genetics Infrastructure RNASeq SNP Sequencing
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.12.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicAlignments")

Popular man pages

cigar-utils: CIGAR utility functions
findSpliceOverlaps-methods: Classify ranges (reads) as compatible with existing genomic...
GAlignmentPairs-class: GAlignmentPairs objects
GAlignments-class: GAlignments objects
GAlignmentsList-class: GAlignmentsList objects
readGAlignments: Reading genomic alignments from a file
summarizeOverlaps-methods: Perform overlap queries between reads and genomic features
See all...

All man pages Function index File listing

Man pages

cigar-utils: CIGAR utility functions
coordinate-mapping-methods: Map range coordinates between reads and genome space using...
coverage-methods: Coverage of a GAlignments, GAlignmentPairs, or...
encodeOverlaps-methods: Encode the overlaps between RNA-seq reads and the transcripts...
findCompatibleOverlaps-methods: Finding hits between reads and transcripts that are...
findMateAlignment: Pairing the elements of a GAlignments object
findOverlaps-methods: Finding overlapping genomic alignments
findSpliceOverlaps-methods: Classify ranges (reads) as compatible with existing genomic...
GAlignmentPairs-class: GAlignmentPairs objects
GAlignments-class: GAlignments objects
GAlignmentsList-class: GAlignmentsList objects
GappedReads-class: (Legacy) GappedReads objects
intra-range-methods: Intra range transformations of a GAlignments or...
junctions-methods: Extract junctions from genomic alignments
OverlapEncodings-class: OverlapEncodings objects
pileLettersAt: Pile the letters of a set of aligned reads on top of a set of...
readGAlignments: Reading genomic alignments from a file
sequenceLayer: Lay read sequences alongside the reference space, using their...
setops-methods: Set operations on GAlignments objects
stackStringsFromBam: Stack the read sequences stored in a BAM file on a region of...
summarizeOverlaps-methods: Perform overlap queries between reads and genomic features

Functions

CIGAR_OPS Man page
D_and_N_ranges_on_query_space Source code
D_ranges_on_query_space Source code
GAlignmentPairs Man page Source code
GAlignmentPairs-class Man page
GAlignmentPairs.getElement Source code
GAlignments Man page Source code
GAlignments-class Man page
GAlignmentsList Man page Man page Source code
GAlignmentsList-class Man page
GAlignmentsORGAlignmentPairs.findCompatibleOverlaps Source code
GRangesList_encodeOverlaps Source code
GappedReads Man page Source code
GappedReads-class Man page
Hits_encode_overlaps Source code
IntersectionNotEmpty Man page Source code
IntersectionStrict Man page Source code
Lencoding Man page Source code
Lnjunc Man page Source code
Loffset Man page
Loffset,OverlapEncodings-method Man page
NATURAL_INTRON_MOTIFS Man page
N_ranges_on_query_space Source code
OverlapEncodings Man page
OverlapEncodings-class Man page
RangesList_encodeOverlaps Source code
RangesList_encode_overlaps Source code
Rencoding Man page Source code
Rnjunc Man page Source code
Roffset Man page
Roffset,OverlapEncodings-method Man page
Union Man page Source code
[[,GAlignmentPairs,ANY,ANY-method Man page
allMatch Source code
alphabetFrequencyFromBam Man page Source code
as.data.frame,GAlignments-method Man page
as.data.frame,OverlapEncodings-method Man page
as.data.frame.OverlapEncodings Man page Source code
asFactorRle Source code
bed_to_Juncs Source code
bindExtraData Source code
build_CompatibleWithSkippedExons_pattern Source code
build_CompatibleWithSkippedExons_pattern0 Source code
build_compatible_encoding_pattern Source code
build_compatible_encoding_subpatterns Source code
c,GAlignmentPairs-method Man page
c,GAlignments-method Man page
c,GAlignmentsList-method Man page
c,GappedReads-method Man page
checkArgs Source code
checkMetadatacols Source code
cigar Man page
cigar,GAlignments-method Man page
cigar,GAlignmentsList-method Man page
cigar-utils Man page
cigarNarrow Man page Source code
cigarOpTable Man page Source code
cigarQNarrow Man page Source code
cigarRangesAlongPairwiseSpace Man page Source code
cigarRangesAlongQuerySpace Man page Source code
cigarRangesAlongReferenceSpace Man page Source code
cigarToRleList Man page Source code
cigarWidthAlongPairwiseSpace Man page Source code
cigarWidthAlongQuerySpace Man page Source code
cigarWidthAlongReferenceSpace Man page Source code
cigar_ranges Source code
cigar_width Source code
class:GAlignmentPairs Man page
class:GAlignments Man page
class:GAlignmentsList Man page
class:GappedReads Man page
class:OverlapEncodings Man page
coerce,GAlignmentPairs,GAlignments-method Man page
coerce,GAlignmentPairs,GAlignmentsList-method Man page
coerce,GAlignmentPairs,GRanges-method Man page
coerce,GAlignmentPairs,GRangesList-method Man page
coerce,GAlignmentPairs,Ranges-method Man page
coerce,GAlignments,GRanges-method Man page
coerce,GAlignments,GRangesList-method Man page
coerce,GAlignments,Ranges-method Man page
coerce,GAlignments,RangesList-method Man page
coerce,GAlignmentsList,GRanges-method Man page
coerce,GAlignmentsList,GRangesList-method Man page
coerce,GAlignmentsList,Ranges-method Man page
coerce,GAlignmentsList,RangesList-method Man page
coerce,GenomicRanges,GAlignments-method Man page
combineBamFlagFilters Source code
combine_GAlignmentPairs_objects Source code
combine_GAlignments_objects Source code
compatibleTranscription Source code
coordinate-mapping-methods Man page
countCompatibleOverlaps Man page Source code
countDumpedAlignments Man page Source code
countWithYieldSize Source code
coverage Man page
coverage,BamFile-method Man page
coverage,GAlignmentPairs-method Man page
coverage,GAlignments-method Man page
coverage,GAlignmentsList-method Man page
coverage,character-method Man page
coverage-methods Man page
dispatchBamFiles Source code
dispatchOverlaps Source code
dumpAlignments Source code
dumpEnvir Source code
elementMetadata,GAlignmentsList-method Man page
elementMetadata<-,GAlignmentsList-method Man page
encodeOverlaps Man page
encodeOverlaps,GRangesList,GRangesList-method Man page
encodeOverlaps,Ranges,RangesList-method Man page
encodeOverlaps,RangesList,Ranges-method Man page
encodeOverlaps,RangesList,RangesList-method Man page
encodeOverlaps-methods Man page
encodeOverlaps1 Man page Source code
encoding,OverlapEncodings-method Man page
encodingHalves Man page
encodingHalves,OverlapEncodings-method Man page
encodingHalves,character-method Man page
encodingHalves,factor-method Man page
end,GAlignments-method Man page
end,GAlignmentsList-method Man page
error_on_discordant_seqnames Source code
explodeCigarOpLengths Man page Source code
explodeCigarOps Man page Source code
extractAlignmentRangesOnReference Man page Source code
extractQueryStartInTranscript Man page Source code
extractSkippedExonRanks Man page
extractSkippedExonRanks,OverlapEncodings-method Man page
extractSkippedExonRanks,character-method Man page
extractSkippedExonRanks,factor-method Man page
extractSpannedExonRanks Man page
extractSpannedExonRanks,OverlapEncodings-method Man page
extractSpannedExonRanks,character-method Man page
extractSpannedExonRanks,factor-method Man page
extractSteppedExonRanks Man page Source code
extractSteppedExonRanks,OverlapEncodings-method Man page
extractSteppedExonRanks,character-method Man page
extractSteppedExonRanks,factor-method Man page
extractSteppedExonRanksFromEncodingBlocks Source code
extract_njunc_from_encoding Source code
extract_unoriented_intron_motif Source code
fillJunctionGaps Source code
findCompatibleOverlaps Man page
findCompatibleOverlaps,GAlignmentPairs,GRangesList-method Man page
findCompatibleOverlaps,GAlignments,GRangesList-method Man page
findCompatibleOverlaps-methods Man page
findMateAlignment Man page Source code
findOverlaps Man page
findOverlaps,GAlignmentPairs,GAlignmentPairs-method Man page
findOverlaps,GAlignmentPairs,Vector-method Man page
findOverlaps,GAlignments,GAlignments-method Man page
findOverlaps,GAlignments,Vector-method Man page
findOverlaps,GAlignmentsList,GAlignmentsList-method Man page
findOverlaps,GAlignmentsList,Vector-method Man page
findOverlaps,Vector,GAlignmentPairs-method Man page
findOverlaps,Vector,GAlignments-method Man page
findOverlaps,Vector,GAlignmentsList-method Man page
findOverlaps-methods Man page
findRangesOverlaps Source code
findSpliceOverlaps Man page Source code
findSpliceOverlaps,BamFile,ANY-method Man page
findSpliceOverlaps,GAlignmentPairs,GRangesList-method Man page
findSpliceOverlaps,GAlignments,GRangesList-method Man page
findSpliceOverlaps,GRangesList,GRangesList-method Man page
findSpliceOverlaps,character,ANY-method Man page
findSpliceOverlaps-methods Man page
first Man page
first,GAlignmentPairs-method Man page
first_strand Source code
flipQuery Man page Source code
flippedQuery Man page
flippedQuery,OverlapEncodings-method Man page
flushDumpedAlignments Man page Source code
gaps Source code
getCharacterOrderAndGroupSizes Source code
getDumpedAlignments Man page Source code
getReadFunction Source code
get_GRangesList_spaces Source code
get_GRanges_spaces Source code
get_STAR_intron_motif_levels Source code
granges,GAlignmentPairs-method Man page
granges,GAlignments-method Man page
granges,GAlignmentsList-method Man page
grglist,GAlignmentPairs-method Man page
grglist,GAlignments-method Man page
grglist,GAlignmentsList-method Man page
hasDuplicates Source code
intra-range-methods Man page
invertStrand,GAlignmentPairs-method Man page
is.unsorted,GAlignments-method Man page
isCompatibleWithSkippedExons Man page
isCompatibleWithSkippedExons,OverlapEncodings-method Man page
isCompatibleWithSkippedExons,character-method Man page
isCompatibleWithSkippedExons,factor-method Man page
isCompatibleWithSplicing Man page
isCompatibleWithSplicing,OverlapEncodings-method Man page
isCompatibleWithSplicing,character-method Man page
isCompatibleWithSplicing,factor-method Man page
isProperPair Man page
isProperPair,GAlignmentPairs-method Man page
junctions Man page
junctions,GAlignmentPairs-method Man page
junctions,GAlignments-method Man page
junctions,GAlignmentsList-method Man page
junctions-methods Man page
last Man page
last,GAlignmentPairs-method Man page
last_strand Source code
length,GAlignmentPairs-method Man page
length,GAlignments-method Man page
levels,OverlapEncodings-method Man page
levels.OverlapEncodings Man page Source code
load_bamcols_from_BamFile Source code
load_seqlengths_from_BamFile Source code
makeFlagBitmask Source code
makeGAlignmentPairs Man page Source code
makeGAlignmentsGNames Source code
makeMateIdx2 Source code
makeNakedMatFromGAlignmentPairs Source code
makeNakedMatFromGAlignments Source code
make_D_and_N_fillers Source code
make_GAlignmentPairs_from_GAlignments Source code
make_GRangesList_from_CompressedIRangesList Source code
make_empty_sequences Source code
make_fillers Source code
make_it_real Source code
make_naked_matrix_from_OverlapEncodings Source code
make_sequence_fillers_from_list_of_widths Source code
make_sequence_fillers_from_widths Source code
make_split_GRanges_from_GAlignmentPairs Source code
make_split_IRanges_from_GAlignmentPairs Source code
mapFromAlignments Man page Source code
mapFromAlignments,GenomicRanges,GAlignments-method Man page
mapFromAlignments,Ranges,GAlignments-method Man page
mapToAlignments Man page Source code
mapToAlignments,GenomicRanges,GAlignments-method Man page
mapToAlignments,Ranges,GAlignments-method Man page
matesFromBam Source code
names,GAlignmentPairs-method Man page
names,GAlignments-method Man page
names,GAlignmentsList-method Man page
names<-,GAlignmentPairs-method Man page
names<-,GAlignments-method Man page
names<-,GAlignmentsList-method Man page
narrow Man page
narrow,GAlignments-method Man page
narrow,GAlignmentsList-method Man page
narrow,GappedReads-method Man page
narrowGAlignments Source code
nfer_intron_strand Source code
njunc Man page
njunc,ANY-method Man page
njunc,GAlignmentPairs-method Man page
njunc,GAlignments-method Man page
njunc,GAlignmentsList-method Man page
njunc_single_end_encodings Source code
normargParam Source code
normarg_cigar Source code
normarg_flag Source code
normarg_ops Source code
normarg_param Source code
normarg_pos Source code
normarg_strandMode_replace_value Source code
novelBounds Source code
novelExon Source code
novelRetention Source code
novelSpliceEvent Source code
nsertGaps Source code
ntronicRegions Source code
onUnload Source code
oneMatch Source code
oneValPerTopLevelElt Source code
open_BamFile Source code
order,GAlignments-method Man page
orient_intron_motif Source code
parallelSlotNames,OverlapEncodings-method Man page
pcombine Source code
pcompare,GAlignments,GAlignments-method Man page
pileLettersAt Man page Source code
pileLettersOnSingleRefAt Source code
pintersect Man page
pintersect,GAlignments,GRanges-method Man page
pintersect,GRanges,GAlignments-method Man page
pmapAlignments Source code
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,GAlignments-method Man page
qnarrow,GAlignmentsList-method Man page
qnarrow,GappedReads-method Man page
qseq Man page
qseq,GappedReads-method Man page
queryLoc2refLoc Man page Source code
queryLocs2refLocs Man page Source code
qwidth Man page
qwidth,GAlignments-method Man page
qwidth,GAlignmentsList-method Man page
qwidth,GappedReads-method Man page
rangeForSorted Source code
ranges,GAlignmentPairs-method Man page
ranges,GAlignments-method Man page
ranges,GAlignmentsList-method Man page
rank,GAlignments-method Man page
readGAlignmentPairs Man page
readGAlignmentPairs,BamFile-method Man page
readGAlignmentPairs,character-method Man page
readGAlignmentPairs.BamFile Source code
readGAlignments Man page
readGAlignments,BamFile-method Man page
readGAlignments,BamViews-method Man page
readGAlignments,character-method Man page
readGAlignments.BamFile Source code
readGAlignmentsList Man page
readGAlignmentsList,BamFile-method Man page
readGAlignmentsList,character-method Man page
readGAlignmentsList.BamFile Source code
readGappedReads Man page
readGappedReads,BamFile-method Man page
readGappedReads,character-method Man page
readGappedReads.BamFile Source code
readRanges Source code
readSTARJunctions Man page Source code
readTopHatJunctions Man page Source code
relistToClass,GAlignments-method Man page
removeSharedRegions Source code
result Source code
rglist,GAlignments-method Man page
rglist,GAlignmentsList-method Man page
rname Man page
rname,GAlignments-method Man page
rname,GAlignmentsList-method Man page
rname<- Man page
rname<-,GAlignments-method Man page
rname<-,GAlignmentsList-method Man page
sCompatibleWithSkippedExons Source code
sFirstSegment.GAlignments Source code
sFirstSegment.integer Source code
sFirstSegment.matrix Source code
sLastSegment.GAlignments Source code
sLastSegment.integer Source code
sLastSegment.matrix Source code
sWrongStrand Source code
s_compatible_with_splicing Source code
second Man page
second,GAlignmentPairs-method Man page
selectEncodingWithCompatibleStrand Man page Source code
select_pairwise_space Source code
select_query_space Source code
select_reference_space Source code
seqinfo,GAlignmentPairs-method Man page
seqinfo,GAlignments-method Man page
seqinfo,GAlignmentsList-method Man page
seqinfo<-,GAlignmentPairs-method Man page
seqinfo<-,GAlignments-method Man page
seqinfo<-,GAlignmentsList-method Man page
seqlevelsInUse,GAlignmentPairs-method Man page
seqnames,GAlignmentPairs-method Man page
seqnames,GAlignments-method Man page
seqnames,GAlignmentsList-method Man page
seqnames<-,GAlignments-method Man page
seqnames<-,GAlignmentsList-method Man page
sequenceLayer Man page Source code
setElementNROWS Source code
set_GAlignments_seqinfo Source code
setops-methods Man page
show,GAlignmentPairs-method Man page
show,GAlignments-method Man page
show,GAlignmentsList-method Man page
show,OverlapEncodings-method Man page
showGAlignmentPairs Source code
showGAlignments Source code
showGAlignmentsEltsWithMoreThan1Mate Source code
showOverlapEncodings Source code
shrinkByHalf Source code
sort,GAlignments-method Man page
spliceEvent Source code
split_encoding_halves Source code
stackStringsFromBam Man page Source code
start,GAlignments-method Man page
start,GAlignmentsList-method Man page
strand,GAlignmentPairs-method Man page
strand,GAlignments-method Man page
strand,GAlignmentsList-method Man page
strand<-,GAlignments-method Man page
strand<-,GAlignmentsList,character-method Man page
strand<-,GAlignmentsList-method Man page
strandMode Man page
strandMode,GAlignmentPairs-method Man page
strandMode<- Man page
strandMode<-,GAlignmentPairs-method Man page
summarizeJunctions Man page Source code
summarizeOverlaps Man page Source code
summarizeOverlaps,BamViews,missing-method Man page
summarizeOverlaps,GRanges,BamFile-method Man page
summarizeOverlaps,GRanges,BamFileList-method Man page
summarizeOverlaps,GRanges,GAlignmentPairs-method Man page
summarizeOverlaps,GRanges,GAlignments-method Man page
summarizeOverlaps,GRanges,GAlignmentsList-method Man page
summarizeOverlaps,GRanges,GRanges-method Man page
summarizeOverlaps,GRanges,GRangesList-method Man page
summarizeOverlaps,GRanges,character-method Man page
summarizeOverlaps,GRangesList,BamFile-method Man page
summarizeOverlaps,GRangesList,BamFileList-method Man page
summarizeOverlaps,GRangesList,GAlignmentPairs-method Man page
summarizeOverlaps,GRangesList,GAlignments-method Man page
summarizeOverlaps,GRangesList,GAlignmentsList-method Man page
summarizeOverlaps,GRangesList,GRanges-method Man page
summarizeOverlaps,GRangesList,GRangesList-method Man page
summarizeOverlaps,GRangesList,character-method Man page
summarizeOverlaps-methods Man page
summarizeOverlaps_BamFileList Source code
summarizeOverlaps_character Source code
test Source code
unlist,GAlignmentPairs-method Man page
updateObject,GAlignments-method Man page
updateObject,GAlignmentsList-method Man page
valid.GAlignmentPairs Source code
valid.GAlignmentPairs.first Source code
valid.GAlignmentPairs.isProperPair Source code
valid.GAlignmentPairs.last Source code
valid.GAlignmentPairs.names Source code
valid.GAlignmentPairs.strandMode Source code
valid.GAlignments Source code
valid.GAlignments.cigar Source code
valid.GAlignments.names Source code
valid.GAlignments.seqnames Source code
valid.GAlignments.start Source code
valid.GAlignments.strand Source code
valid.GAlignmentsList Source code
valid.GappedReads Source code
valid.GappedReads.qseq Source code
validCigar Man page Source code
width,GAlignments-method Man page
width,GAlignmentsList-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/GAlignmentPairs-class.R
R/GAlignments-class.R
R/GAlignmentsList-class.R
R/GappedReads-class.R
R/OverlapEncodings-class.R
R/cigar-utils.R
R/coordinate-mapping-methods.R
R/coverage-methods.R
R/encodeOverlaps-methods.R
R/findCompatibleOverlaps-methods.R
R/findMateAlignment.R
R/findOverlaps-methods.R
R/findSpliceOverlaps-methods.R
R/intra-range-methods.R
R/junctions-methods.R
R/pileLettersAt.R
R/readGAlignments.R
R/sequenceLayer.R
R/setops-methods.R
R/stackStringsFromBam.R
R/summarizeOverlaps-methods.R
R/zzz.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/GenomicAlignmentsIntroduction.R
inst/doc/GenomicAlignmentsIntroduction.Rnw
inst/doc/GenomicAlignmentsIntroduction.pdf
inst/doc/OverlapEncodings.R
inst/doc/OverlapEncodings.Rnw
inst/doc/OverlapEncodings.pdf
inst/doc/WorkingWithAlignedNucleotides.R
inst/doc/WorkingWithAlignedNucleotides.Rnw
inst/doc/WorkingWithAlignedNucleotides.pdf
inst/doc/summarizeOverlaps.R
inst/doc/summarizeOverlaps.Rnw
inst/doc/summarizeOverlaps.pdf
inst/extdata
inst/extdata/sm_treated1.bam
inst/extdata/sm_untreated1.bam
inst/unitTests
inst/unitTests/test_GAlignments-class.R
inst/unitTests/test_GAlignmentsList-class.R
inst/unitTests/test_cigar-utils.R
inst/unitTests/test_coordinate-mapping-methods.R
inst/unitTests/test_findSpliceOverlaps-methods.R
inst/unitTests/test_intra-range-methods.R
inst/unitTests/test_readGAlignmentPairs.R
inst/unitTests/test_readGAlignments.R
inst/unitTests/test_readGAlignmentsList.R
inst/unitTests/test_summarizeOverlaps-methods.R
man
man/GAlignmentPairs-class.Rd
man/GAlignments-class.Rd
man/GAlignmentsList-class.Rd
man/GappedReads-class.Rd
man/OverlapEncodings-class.Rd
man/cigar-utils.Rd
man/coordinate-mapping-methods.Rd
man/coverage-methods.Rd
man/encodeOverlaps-methods.Rd
man/findCompatibleOverlaps-methods.Rd
man/findMateAlignment.Rd
man/findOverlaps-methods.Rd
man/findSpliceOverlaps-methods.Rd
man/intra-range-methods.Rd
man/junctions-methods.Rd
man/pileLettersAt.Rd
man/readGAlignments.Rd
man/sequenceLayer.Rd
man/setops-methods.Rd
man/stackStringsFromBam.Rd
man/summarizeOverlaps-methods.Rd
src
src/GenomicAlignments.h
src/IRanges_stubs.c
src/R_init_GenomicAlignments.c
src/S4Vectors_stubs.c
src/cigar_utils.c
src/coordinate_mapping_methods.c
src/encodeOverlaps_methods.c
tests
tests/run_unitTests.R
vignettes
vignettes/GenomicAlignmentsIntroduction.Rnw
vignettes/OverlapEncodings.Rnw
vignettes/WorkingWithAlignedNucleotides.Rnw
vignettes/precomputed_results
vignettes/precomputed_results/U1.sbcompHITSa.rda
vignettes/precomputed_results/U1.sbcompHITSb.rda
vignettes/precomputed_results/exbytx.rda
vignettes/summarizeOverlaps-modes.pdf
vignettes/summarizeOverlaps.Rnw
GenomicAlignments documentation built on May 20, 2017, 9:12 p.m.

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