rtracklayer
R interface to genome annotation files and the UCSC genome browser

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Source code
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Man pages
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rtracklayer: R interface to genome annotation files and the UCSC genome browser
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API

API for rtracklayer
R interface to genome annotation files and the UCSC genome browser

Global functions
$,Quickload-method Man page
$,TrackDb-method Man page
$,TrackHub-method Man page
$<-,TrackDb-method Man page
.DNAString_to_twoBit Source code
.TwoBits_export Source code
.exportToQuickload Source code
.exportToTrackHub Source code
.export_SimpleGRangesList_RTLFile Source code
.getOrganism Source code
.get_version_from_pragmas Source code
.is_multi_tag Source code
.make_filexp_from_filepath Source code
.normarg_filter Source code
.normarg_version Source code
.onLoad Source code
.onUnload Source code
.parseSequenceRegionsAsSeqinfo Source code
.parseSpeciesAsMetadata Source code
.parseURI Source code
.prepare_colmap_and_tags Source code
.seqlengths_TwoBitFile Source code
.sniffGFFVersion Source code
.strsplit_cols Source code
.test Source code
.uploadTableBrowserRanges Source code
.url_decode_cols Source code
.validateColNames Source code
.wigWriter Source code
2BitFile Man page
2BitFile-class Man page
BBFile Man page
BBFile-class Man page
BED15File Man page Source code
BED15File-class Man page
BEDFile Man page Source code
BEDFile-class Man page
BEDGraphFile Man page Source code
BEDGraphFile-class Man page
BEDPEFile Man page Source code
BEDPEFile-class Man page
BGZFile Source code
BSGenomeForID Source code
BWFile Man page
BWFile-class Man page
BZ2File Source code
BasicTrackLine-class Man page
Bed15TrackLine-class Man page
BigBedFile Man page Source code
BigBedFile-class Man page
BigBedSelection Man page Source code
BigBedSelection-class Man page
BigWigFile Man page Source code
BigWigFile-class Man page
BigWigFileList Man page Source code
BigWigFileList-class Man page
BigWigSelection Man page Source code
BigWigSelection-class Man page
BroadPeakFile Man page Source code
BroadPeakFile-class Man page
BrowserSession-class Man page
BrowserView-class Man page
BrowserViewList Man page Source code
BrowserViewList-class Man page
Chain-class Man page
ChainBlock-class Man page
ChainFile Man page Source code
ChainFile-class Man page
CompressedFile-class Man page
FastaFile Man page Source code
FastaFile-class Man page
FileForFormat Man page Source code
GFF1File Man page Source code
GFF1File-class Man page
GFF2File Man page Source code
GFF2File-class Man page
GFF3File Man page Source code
GFF3File-class Man page
GFFFile Man page Source code
GFFFile-class Man page
GFFcolnames Man page Source code
GRangesForBSGenome Man page Source code
GRangesForGenome Source code
GRangesForUCSCGenome Man page Source code
GTFFile Man page Source code
GTFFile-class Man page
GVFFile Man page Source code
GVFFile-class Man page
GZFile Source code
Genome Source code
GenomeContainer Source code
GenomicData Man page Source code
GenomicSelection Man page Source code
GraphTrackLine-class Man page
IntegerRangesList-methods Man page
NarrowPeakFile Man page Source code
NarrowPeakFile-class Man page
Quickload Man page Source code
Quickload-class Man page
QuickloadGenome Man page Source code
QuickloadGenome-class Man page
QuickloadGenome_annotFiles Source code
Quickload_contents Source code
RTLFile-class Man page
RTLFileList Source code
RTLFileList-class Man page
SeqinfoForBSGenome Man page Source code
SeqinfoForUCSCGenome Man page Source code
TabSeparatedFile Source code
Track Source code
TrackContainer Source code
TrackDb-class Man page
TrackHub Man page Source code
TrackHub-class Man page
TrackHubGenome Man page Source code
TrackHubGenome-class Man page
TrackLine-class Man page
TwoBitFile Man page Source code
TwoBitFile-class Man page
UCSCData Source code
UCSCData-class Man page
UCSCFile Man page Source code
UCSCFile-class Man page
UCSCSchema-class Man page
UCSCSession-class Man page
UCSCTableQuery-class Man page
UCSCTrackModes-class Man page
UCSCView-class Man page
WIGFile Man page Source code
WIGFile-class Man page
XZFile Source code
[,UCSCTrackModes,ANY,ANY,ANY-method Man page
[<-,UCSCTrackModes,ANY,ANY,ANY-method Man page
[[,Quickload,ANY,ANY-method Man page
[[,TrackDb,ANY,ANY-method Man page
[[,TrackHub,ANY,ANY-method Man page
[[<-,TrackDb,ANY,ANY-method Man page
`resource<-` Source code
activeView Man page
activeView,BrowserSession-method Man page
activeView,UCSCView-method Man page
activeView-methods Man page
activeView<- Man page
activeView<--methods Man page
addGenomeToContents Source code
annotsFile Source code
as.character,RTLFile-method Man page
asBED Man page
asBED,GAlignments-method Man page
asBED,GRangesList-method Man page
asGFF Man page
asGFF,GRangesList-method Man page
asGFFVersion Source code
autoSqlString Source code
bedString Source code
blocks Man page
blocks,GenomicRanges-method Man page
blocks-methods Man page
browseGenome Man page
browseGenome,GenomicRanges_OR_GenomicRangesList-method Man page
browseGenome,missing-method Man page
browserSession Man page
browserSession,BrowserView-method Man page
browserSession,UCSCTableQuery-method Man page
browserSession,character-method Man page
browserSession,missing-method Man page
browserSession-methods Man page
browserSession<- Man page
browserSession<-,UCSCTableQuery,UCSCSession-method Man page
browserView Man page
browserView,UCSCSession-method Man page
browserView-methods Man page
browserViews Man page
browserViews,UCSCSession-method Man page
browserViews-methods Man page
checkArgFormat Source code
chooseGraphType Source code
chrom Man page
chrom,GRanges-method Man page
chrom,IntegerRangesList-method Man page
chrom<- Man page
chrom<-,GRanges-method Man page
chrom<-,IntegerRangesList-method Man page
class:2BitFile Man page
class:BBFile Man page
class:BED15File Man page
class:BEDFile Man page
class:BEDGraphFile Man page
class:BWFile Man page
class:BigBedFile Man page
class:BigWigFile Man page
class:BigWigFileList Man page
class:BroadPeakFile Man page
class:Chain Man page
class:ChainBlock Man page
class:ChainFile Man page
class:CompressedFile Man page
class:FastaFile Man page
class:GFF1File Man page
class:GFF2File Man page
class:GFF3File Man page
class:GFFFile Man page
class:GTFFile Man page
class:GVFFile Man page
class:NarrowPeakFile Man page
class:Quickload Man page
class:QuickloadGenome Man page
class:RTLFile Man page
class:TrackDb Man page
class:TrackHub Man page
class:TrackHubGenome Man page
class:TwoBitFile Man page
class:UCSCFile Man page
class:WIGFile Man page
cleanupBigWigCache Man page Source code
coerce,BasicTrackLine,GraphTrackLine-method Man page
coerce,BasicTrackLine,character-method Man page
coerce,Bed15TrackLine,character-method Man page
coerce,GRanges,UCSCData-method Man page
coerce,GenomicRanges,BigBedSelection-method Man page
coerce,GenomicRanges,BigWigSelection-method Man page
coerce,GraphTrackLine,BasicTrackLine-method Man page
coerce,GraphTrackLine,character-method Man page
coerce,IntegerRangesList,BigBedSelection-method Man page
coerce,IntegerRangesList,BigWigSelection-method Man page
coerce,TrackLine,character-method Man page
coerce,UCSCData,GRanges-method Man page
coerce,character,BasicTrackLine-method Man page
coerce,character,Bed15TrackLine-method Man page
coerce,character,GraphTrackLine-method Man page
coerce,character,Quickload-method Man page
coerce,character,TrackHub-method Man page
coerce,character,TrackLine-method Man page
combineURI Source code
connection Source code
connectionForResource Source code
contentsFile Source code
copyResourceToQuickload Source code
copyResourceToTrackHub Source code
cpneTrack Man page
createQuickloadGenome Source code
createResource Source code
createTrack Source code
descriptionUrl,TrackHub-method Man page
descriptionUrl<-,TrackHub-method Man page
dropCookie Source code
email,TrackHub-method Man page
email<-,TrackHub-method Man page
expandPath Source code
expandURL Source code
export Man page
export,ANY,BEDFile,ANY-method Man page
export,ANY,BEDPEFile,ANY-method Man page
export,ANY,BamFile,ANY-method Man page
export,ANY,BigBedFile,ANY-method Man page
export,ANY,BigWigFile,ANY-method Man page
export,ANY,CompressedFile,missing-method Man page
export,ANY,FastaFile,ANY-method Man page
export,ANY,GFFFile,ANY-method Man page
export,ANY,TabSeparatedFile,ANY-method Man page
export,ANY,TwoBitFile,ANY-method Man page
export,ANY,UCSCFile,ANY-method Man page
export,ANY,WIGFile,ANY-method Man page
export,ANY,character,character-method Man page
export,ANY,character,missing-method Man page
export,ANY,connection,character-method Man page
export,ANY,connection,missing-method Man page
export,ANY,missing,character-method Man page
export,DNAStringSet,TwoBitFile,ANY-method Man page
export,DNAStringSet,character,ANY-method Man page
export,GAlignmentPairs,BamFile,ANY-method Man page
export,GAlignments,BamFile,ANY-method Man page
export,GRangesList,BEDFile,ANY-method Man page
export,GRangesList,GFFFile,ANY-method Man page
export,GRangesList,GTFFile,ANY-method Man page
export,GenomicRanges,BED15File,ANY-method Man page
export,GenomicRanges,BEDFile,ANY-method Man page
export,GenomicRanges,BigBedFile,ANY-method Man page
export,GenomicRanges,BigWigFile,ANY-method Man page
export,GenomicRanges,GFFFile,ANY-method Man page
export,GenomicRanges,TabSeparatedFile,ANY-method Man page
export,GenomicRanges,UCSCFile,ANY-method Man page
export,GenomicRanges,WIGFile,ANY-method Man page
export,GenomicRangesList,BEDFile,ANY-method Man page
export,GenomicRangesList,GFFFile,ANY-method Man page
export,GenomicRangesList,UCSCFile,ANY-method Man page
export,GenomicRangesList,WIGFile,ANY-method Man page
export,List,BigWigFile,ANY-method Man page
export,Pairs,BEDPEFile,ANY-method Man page
export,UCSCData,BED15File,ANY-method Man page
export,UCSCData,BEDFile,ANY-method Man page
export,UCSCData,UCSCFile,ANY-method Man page
export,UCSCData,WIGFile,ANY-method Man page
export,XStringSet,FastaFile,ANY-method Man page
export.2bit Man page
export.2bit,ANY-method Man page
export.bb Man page
export.bb,ANY-method Man page
export.bed Man page
export.bed,ANY-method Man page
export.bed,UCSCData,character_OR_connection-method Man page
export.bed15 Man page
export.bed15,ANY-method Man page
export.bed15,UCSCData-method Man page
export.bedGraph Man page
export.bedGraph,ANY-method Man page
export.bw Man page
export.bw,ANY-method Man page
export.gff Man page
export.gff,ANY-method Man page
export.gff,UCSCData,character_OR_connection-method Man page
export.gff1 Man page
export.gff1,ANY-method Man page
export.gff2 Man page
export.gff2,ANY-method Man page
export.gff3 Man page
export.gff3,ANY-method Man page
export.ucsc Man page
export.ucsc,ANY,ANY-method Man page
export.ucsc,ANY,RTLFile-method Man page
export.ucsc,UCSCData,character_OR_connection-method Man page
export.wig Man page
export.wig,ANY-method Man page
exportToTabix Man page
exportToTabix,ANY,character-method Man page
fastaSeqnames Source code
fileFormat Man page
fileFormat,CompressedFile-method Man page
fileFormat,RTLFile-method Man page
fileFormat,character-method Man page
fillColumn Source code
firstTableName Source code
flipStrandSimple Source code
flipStrandTricky Source code
formatDescription Man page
formatDescription,UCSCSchema-method Man page
frame Source code
genome,BrowserSession-method Man page
genome,GFFFile-method Man page
genome,Quickload-method Man page
genome,QuickloadGenome-method Man page
genome,TrackHub-method Man page
genome,TrackHubGenome-method Man page
genome,UCSCSchema-method Man page Man page
genome,UCSCSession-method Man page
genome,ucscCart-method Man page
genome<-,BrowserSession-method Man page
genome<-,UCSCSession-method Man page
genomeBrowsers Man page Source code
genomeField,TrackHub-method Man page
genomeField<-,TrackHub-method Man page
genomeFile Source code
genomeFile,TrackHub-method Man page
genomeFile<-,TrackHub-method Man page
genomeInfo,TrackHub-method Man page
genomeInfo<-,TrackHub-method Man page
getGenome Source code
getGenomesContent Source code
getHubContent Source code
getSeq,TwoBitFile-method Man page
getTabCountList Source code
getTable Man page
getTable,UCSCSession-method Man page
getTable,UCSCTableQuery-method Man page
getTableNames Source code
getTrackDbContent Source code
getTracks,TrackHubGenome-method Man page
gffComment Source code
gffFileClass Source code
gffFileVersion Source code
gffGenomeBuild Source code
handleCategory Source code
handleError Source code
htmlErrorHandler Source code
htmlParse Source code
httpGet Source code
httpPost Source code
httpShow Source code
hub,TrackHub-method Man page
hub<-,TrackHub-method Man page
hubFile Source code
import Man page
import,BED15File,ANY,ANY-method Man page
import,BEDFile,ANY,ANY-method Man page
import,BEDPEFile,ANY,ANY-method Man page
import,BamFile,ANY,ANY-method Man page
import,BigBedFile,ANY,ANY-method Man page
import,BigWigFile,ANY,ANY-method Man page
import,BroadPeakFile,ANY,ANY-method Man page
import,BroadPeakFile,ANY-method Man page
import,ChainFile,ANY,ANY-method Man page
import,CompressedFile,missing,ANY-method Man page
import,FastaFile,ANY,ANY-method Man page
import,GFFFile,ANY,ANY-method Man page
import,NarrowPeakFile,ANY,ANY-method Man page
import,NarrowPeakFile,ANY-method Man page
import,TabixFile,ANY,ANY-method Man page
import,TwoBitFile,ANY,ANY-method Man page
import,UCSCFile,ANY,ANY-method Man page
import,WIGFile,ANY,ANY-method Man page
import,character,character,ANY-method Man page
import,character,missing,ANY-method Man page
import,connection,character,ANY-method Man page
import,connection,missing,ANY-method Man page
import,missing,ANY,character-method Man page
import.2bit Man page
import.2bit,ANY-method Man page
import.BroadPeak Man page
import.BroadPeak,ANY-method Man page
import.NarrowPeak Man page
import.NarrowPeak,ANY-method Man page
import.bb Man page
import.bb,ANY-method Man page
import.bed Man page
import.bed,ANY-method Man page
import.bed15 Man page
import.bed15,ANY-method Man page
import.bedGraph Man page
import.bedGraph,ANY-method Man page
import.bw Man page
import.bw,ANY-method Man page
import.chain Man page
import.chain,ANY-method Man page
import.gff Man page
import.gff,ANY-method Man page
import.gff1 Man page
import.gff1,ANY-method Man page
import.gff2 Man page
import.gff2,ANY-method Man page
import.gff3 Man page
import.gff3,ANY-method Man page
import.ucsc Man page
import.ucsc,ANY-method Man page
import.ucsc,RTLFile-method Man page
import.wig Man page
import.wig,ANY-method Man page
inconsistentFieldCounts Source code
indexTrack Source code
initialize,UCSCData-method Man page
initialize,UCSCSession-method Man page
isFieldEmpty Source code
isFileReference Source code
isNCBISpeciesURL Source code
isURL Source code
isValidScore Source code
length,Quickload-method Man page
length,QuickloadGenome-method Man page
length,TrackHub-method Man page
length,TrackHubGenome-method Man page
liftOver Man page
liftOver,ANY,ANY-method Man page
liftOver,GenomicRanges,Chain-method Man page
longLabel,TrackHub-method Man page
longLabel<-,TrackHub-method Man page
manage Source code
managed Source code
manager Source code
mcols,QuickloadGenome-method Man page
mergeRange Source code
metadataFromNCBI Source code
names,BrowserSession-method Man page
names,QuickloadGenome-method Man page
names,TrackHubGenome-method Man page
names,UCSCTableQuery-method Man page
names<-,UCSCTableQuery-method Man page
normArgGenome Source code
normArgTable Source code
normArgTrack Source code
normArgTrackData Source code
normGenomeRange Source code
normTableQueryRange Source code
normURI Source code
nrow,UCSCSchema-method Man page
offset,ChainBlock-method Man page
organism,QuickloadGenome-method Man page
organism,TrackHubGenome-method Man page
outputTruncated Source code
parseFormatFromTrackLine Source code
parseOrganismFromNCBI Source code
parseTaxonomyIdFromNCBI Source code
pasteCollapse Source code
path Man page
path,BigWigFileList-method Man page
path,RTLFile-method Man page
queryForConnection Source code
quickload Man page Source code
quickloadGenomeId Source code
range,BrowserSession-method Man page
range,UCSCSession-method Man page
range,UCSCTableQuery-method Man page
range,UCSCView-method Man page
range,ucscCart-method Man page
range<- Man page
range<-,UCSCSession-method Man page
range<-,UCSCTableQuery-method Man page
range<-,UCSCView-method Man page
ranges,ChainBlock-method Man page
readAndSanitize Source code
readGFF Man page Source code
readGFFAsGRanges Source code
readGFFPragmas Source code
readIGVDataFile Source code
readIGVRegistry Source code
rectifyDataFrame Source code
referenceSequence Man page
referenceSequence,QuickloadGenome-method Man page
referenceSequence,TrackHubGenome-method Man page
referenceSequence<- Man page
referenceSequence<-,QuickloadGenome-method Man page
referenceSequence<-,TrackHubGenome-method Man page
referenceSequenceFile Source code
release Source code
releaseDate,QuickloadGenome-method Man page
resolveTrackIndex Source code
resource Man page Source code
resourceDescription Source code
reversed Man page
reversed,ChainBlock-method Man page
scanGFFDirectives Source code
scanTrackLine Source code
score,ANY-method Man page
score,ChainBlock-method Man page
seqinfo,BigBedFile-method Man page
seqinfo,BigWigFile-method Man page
seqinfo,DNAStringSet-method Man page
seqinfo,QuickloadGenome-method Man page
seqinfo,TwoBitFile-method Man page
seqinfo,UCSCSession-method Man page
seqinfo<-,QuickloadGenome-method Man page
seqinfoForGenome Source code
sequence<- Man page
sequence<--methods Man page
setGenome Source code
setGenomesContent Source code
setHubContent Source code
setUserUdcDir Source code
shortLabel,TrackHub-method Man page
shortLabel<-,TrackHub-method Man page
show,BrowserSession-method Man page
show,BrowserView-method Man page
show,Quickload-method Man page
show,QuickloadGenome-method Man page
show,RTLFile-method Man page
show,TrackHub-method Man page
show,TrackHubGenome-method Man page
show,TrackLine-method Man page
show,UCSCData-method Man page
show,UCSCTableQuery-method Man page
singleGenome Source code
smoothGaps Source code
sniffGFFVersion Source code
space,ChainBlock-method Man page
spansGenome Source code
speciesFromNCBI Source code
split,UCSCData,ANY-method Man page
split,UCSCData,Vector-method Man page
splitUCSCData Source code
stopIfNotGenome Source code
stopIfNotLocal Source code
stopIfNotValidForExport Source code
summary,BigWigFile-method Man page
synonymFile Source code
tableHasOutput Source code
tableName Man page
tableName,UCSCSchema-method Man page
tableName,UCSCTableQuery-method Man page
tableName<- Man page
tableName<-,UCSCTableQuery-method Man page
tableNames Man page
tableNames,UCSCTableQuery-method Man page
targets Man page
taxonomyIdFromNCBI Source code
track Man page
track,QuickloadGenome-method Man page
track,TrackHubGenome-method Man page
track,UCSCSession-method Man page
track,UCSCTableQuery-method Man page
track<- Man page
track<-,BrowserSession,ANY-method Man page
track<-,QuickloadGenome,ANY-method Man page
track<-,QuickloadGenome,RTLFile-method Man page
track<-,QuickloadGenome,RsamtoolsFile-method Man page
track<-,QuickloadGenome,character-method Man page
track<-,TrackDb,ANY-method Man page
track<-,TrackHubGenome,ANY-method Man page
track<-,TrackHubGenome,RTLFile-method Man page
track<-,TrackHubGenome,RsamtoolsFile-method Man page
track<-,TrackHubGenome,character-method Man page
track<-,UCSCSession,GenomicRangesList-method Man page
track<-,UCSCSession,RTLFile-method Man page
track<--methods Man page
trackField,TrackHubGenome-method Man page
trackField<-,TrackHubGenome-method Man page
trackLineClass Source code
trackName Man page
trackName,UCSCTableQuery-method Man page
trackName<- Man page
trackName<-,UCSCTableQuery-method Man page
trackNames Man page
trackNames,BrowserSession-method Man page
trackNames,UCSCSession-method Man page
trackNames,UCSCTableQuery-method Man page
trackNames,UCSCTrackModes-method Man page
trackNames,UCSCView-method Man page
trackNames-methods Man page
trackNames<- Man page
trackNames<-,UCSCTrackModes-method Man page
trackNames<-,UCSCView-method Man page
trackNames<--methods Man page
trackhub Man page Source code
trimSlash Source code
twoBitPath Source code
ucscExport Source code
ucscGenomes Man page Source code
ucscGet Source code
ucscPair Source code
ucscParsePairs Source code
ucscPost Source code
ucscSchema Man page
ucscSchema,UCSCSchemaDescription-method Man page
ucscSchema,UCSCTableQuery-method Man page
ucscShow Source code
ucscTableGet Source code
ucscTablePost Source code
ucscTableQuery Man page
ucscTableQuery,UCSCSession-method Man page
ucscTableQuery,character-method Man page
ucscTrackModes Man page
ucscTrackModes,UCSCSession-method Man page
ucscTrackModes,UCSCView-method Man page
ucscTrackModes,character-method Man page
ucscTrackModes,missing-method Man page
ucscTrackModes,ucscTracks-method Man page
ucscTrackModes-methods Man page
ucscTrackModes<- Man page
ucscTrackModes<-,UCSCView,UCSCTrackModes-method Man page
ucscTrackModes<-,UCSCView,character-method Man page
ucscTrackModes<--methods Man page
ucscURL Source code
unmanage Source code
uri Man page Man page
uri,QuickloadGenome-method Man page
uri,TrackHubGenome-method Man page
uriExists Source code
uriIsLocal Source code
uriIsWritable Source code
urlDecode Source code
urlEncode Source code
urlForm Source code
viewURL Man page Source code
visible Man page
visible,BrowserView-method Man page
visible,UCSCView-method Man page
visible<- Man page
visible<-,BrowserView-method Man page
visible<-,UCSCView-method Man page
wigToBigWig Man page Source code
writeTrackHub Man page
writeTrackHub,TrackHubGenome-method Man page
rtracklayer documentation built on Nov. 8, 2020, 6:50 p.m.

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