GenomicAlignments
Representation and manipulation of short genomic alignments

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487
Source code
38
Man pages
21
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GenomicAlignments: Representation and manipulation of short genomic alignments
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API

API for GenomicAlignments
Representation and manipulation of short genomic alignments

Global functions
.D_and_N_ranges_on_query_space Source code
.D_ranges_on_query_space Source code
.GAlignmentPairs.getElement Source code
.GAlignmentsORGAlignmentPairs.findCompatibleOverlaps Source code
.GRangesList_encodeOverlaps Source code
.Hits_encode_overlaps Source code
.N_ranges_on_query_space Source code
.RangesList_encodeOverlaps Source code
.RangesList_encode_overlaps Source code
.allMatch 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
.checkArgs Source code
.checkMetadatacols Source code
.cigar_ranges Source code
.cigar_width Source code
.combineBamFlagFilters Source code
.compatibleTranscription Source code
.countWithYieldSize Source code
.dispatchBamFiles Source code
.dispatchOverlaps Source code
.dumpEnvir Source code
.error_on_discordant_seqnames Source code
.extractSteppedExonRanks Source code
.extractSteppedExonRanksFromEncodingBlocks Source code
.extract_njunc_from_encoding Source code
.extract_unoriented_intron_motif Source code
.findSpliceOverlaps Source code
.first_strand Source code
.from_GAlignments_to_naked_character_matrix_for_display Source code
.gaps Source code
.getCharacterOrderAndGroupSizes Source code
.getReadFunction Source code
.get_GAlignments_version Source code
.get_GRangesList_spaces Source code
.get_GRanges_spaces Source code
.get_STAR_intron_motif_levels Source code
.infer_intron_strand Source code
.insertGaps Source code
.intronicRegions Source code
.isCompatibleWithSkippedExons Source code
.isFirstSegment.GAlignments Source code
.isFirstSegment.integer Source code
.isFirstSegment.matrix Source code
.isLastSegment.GAlignments Source code
.isLastSegment.integer Source code
.isLastSegment.matrix Source code
.isWrongStrand Source code
.is_compatible_with_splicing Source code
.last_strand Source code
.load_bamcols_from_BamFile Source code
.load_seqlengths_from_BamFile Source code
.makeFlagBitmask Source code
.makeGAlignmentsGNames Source code
.makeMateIdx2 Source code
.makeNakedMatFromGAlignmentPairs Source code
.make_D_and_N_fillers Source code
.make_GAlignmentPairs_from_GAlignments 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 Source code
.mapToAlignments Source code
.matesFromBam Source code
.narrowGAlignments Source code
.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
.onUnload Source code
.oneMatch Source code
.oneValPerTopLevelElt Source code
.open_BamFile Source code
.orient_intron_motif Source code
.pcombine Source code
.pileLettersOnSingleRefAt Source code
.pmapAlignments Source code
.rangeForSorted Source code
.readGAlignmentPairs.BamFile Source code
.readGAlignments.BamFile Source code
.readGAlignmentsList.BamFile Source code
.readGappedReads.BamFile Source code
.readRanges Source code
.removeSharedRegions Source code
.result Source code
.select_pairwise_space Source code
.select_query_space Source code
.select_reference_space Source code
.setElementNROWS Source code
.showGAlignmentsEltsWithMoreThan1Mate Source code
.spliceEvent Source code
.split_encoding_halves Source code
.stack_reads Source code
.summarizeOverlaps Source code
.summarizeOverlaps_BamFileList Source code
.summarizeOverlaps_character Source code
.test Source code
.valid.GAlignmentPairs Source code
.valid.GAlignmentPairs.isProperPair Source code
.valid.GAlignmentPairs.seqinfo Source code
.valid.GAlignmentPairs.strandMode Source code
.valid.GAlignments Source code
.valid.GAlignments.cigar 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
CIGAR_OPS Man page
GAlignmentPairs Man page Source code
GAlignmentPairs-class Man page
GAlignments Man page Source code
GAlignments-class Man page
GAlignmentsList Man page Man page Source code
GAlignmentsList-class Man page
GappedReads Man page Source code
GappedReads-class Man page
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
OverlapEncodings Man page
OverlapEncodings-class Man page
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
alphabetFrequencyFromBam Man page Source code
as.data.frame,GAlignmentPairs-method Man page
as.data.frame,GAlignments-method Man page
as.data.frame,OverlapEncodings-method Man page
as.data.frame.OverlapEncodings Man page Source code
bindROWS,GAlignmentPairs-method Man page
bindROWS,GAlignments-method Man page
build_compatible_encoding_subpatterns Source code
c,GappedReads-method Man page
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
class:GAlignmentPairs Man page
class:GAlignments Man page
class:GAlignmentsList Man page
class:GappedReads Man page
class:OverlapEncodings Man page
coerce,GAlignmentPairs,DataFrame-method 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,IntegerRanges-method Man page
coerce,GAlignments,DataFrame-method Man page
coerce,GAlignments,GRanges-method Man page
coerce,GAlignments,GRangesList-method Man page
coerce,GAlignments,IntegerRanges-method Man page
coerce,GAlignments,IntegerRangesList-method Man page
coerce,GAlignmentsList,GAlignmentPairs-method Man page
coerce,GAlignmentsList,GRanges-method Man page
coerce,GAlignmentsList,GRangesList-method Man page
coerce,GAlignmentsList,IntegerRanges-method Man page
coerce,GAlignmentsList,IntegerRangesList-method Man page
coerce,GenomicRanges,GAlignments-method Man page
coerce,list,GAlignmentsList-method Man page
coordinate-mapping-methods Man page
countCompatibleOverlaps Man page Source code
countDumpedAlignments Man page 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
dumpAlignments Source code
elementMetadata,GAlignmentsList-method Man page
elementMetadata<-,GAlignmentsList-method Man page
encodeOverlaps Man page
encodeOverlaps,GRangesList,GRangesList-method Man page
encodeOverlaps,IntegerRanges,IntegerRangesList-method Man page
encodeOverlaps,IntegerRangesList,IntegerRanges-method Man page
encodeOverlaps,IntegerRangesList,IntegerRangesList-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
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
extractSteppedExonRanks,OverlapEncodings-method Man page
extractSteppedExonRanks,character-method Man page
extractSteppedExonRanks,factor-method Man page
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
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
flipQuery Man page Source code
flippedQuery Man page
flippedQuery,OverlapEncodings-method Man page
flushDumpedAlignments Man page Source code
getDumpedAlignments Man page Source code
getListElement,GAlignments-method Man page
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
has_duplicates 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
levels,OverlapEncodings-method Man page
levels.OverlapEncodings Man page Source code
makeGAlignmentPairs Man page Source code
make_GRangesList_from_CompressedIRangesList Source code
mapFromAlignments Man page
mapFromAlignments,GenomicRanges,GAlignments-method Man page
mapFromAlignments,IntegerRanges,GAlignments-method Man page
mapToAlignments Man page
mapToAlignments,GenomicRanges,GAlignments-method Man page
mapToAlignments,IntegerRanges,GAlignments-method Man page
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,GappedReads-method Man page
njunc Man page
njunc,ANY-method Man page
njunc,GAlignmentPairs-method Man page
njunc,GAlignments-method Man page
njunc,GAlignmentsList-method Man page
order,GAlignments-method Man page
parallel_slot_names,GAlignmentPairs-method Man page
parallel_slot_names,GAlignments-method Man page
parallel_slot_names,OverlapEncodings-method Man page
pcompare,GAlignments,GAlignments-method Man page
pileLettersAt Man page Source code
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,IntegerRanges,GAlignments-method Man page
pmapToAlignments Man page
pmapToAlignments,GenomicRanges,GAlignments-method Man page
pmapToAlignments,IntegerRanges,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
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
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 Source code
readTopHatJunctions Man page Source code
relistToClass,GAlignments-method Man page
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
second Man page
second,GAlignmentPairs-method Man page
selectEncodingWithCompatibleStrand Man page 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
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
showOverlapEncodings Source code
shrinkByHalf Source code
sort,GAlignments-method Man page
stackStringsFromBam Man page Source code
stackStringsFromGAlignments Man page Source code
start,GAlignments-method Man page
strand,GAlignmentPairs-method Man page
strand,GAlignments-method Man page
strand,GAlignmentsList-method Man page
strand<-,GAlignments,ANY-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
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
unlist,GAlignmentPairs-method Man page
update,GAlignments-method Man page
updateObject,GAlignments-method Man page
validCigar Man page Source code
width,GAlignments-method Man page
windows,GAlignments-method Man page
GenomicAlignments documentation built on Nov. 8, 2020, 8:12 p.m.

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