Utilities for manipulating chromosome and other 'seqname' identifiers

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Documentation for package ‘GenomeInfoDb’ version 1.6.3

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as.data.frame-method Seqinfo objects
available.species Returns a data.frame that lists the available species strings and their taxonomy Ids.
bsgenomeName GenomeDescription objects
bsgenomeName-method GenomeDescription objects
class:GenomeDescription GenomeDescription objects
class:Seqinfo Seqinfo objects
coerce-method Seqinfo objects
commonName GenomeDescription objects
commonName-method GenomeDescription objects
dropSeqlevels Convenience wrappers to the seqlevels() getter and setter
extractSeqlevels Conveniently rename the seqlevels of an object according to a given style
extractSeqlevelsByGroup Conveniently rename the seqlevels of an object according to a given style
fetchExtendedChromInfoFromUCSC Fetching chromosomes info for some of the UCSC genomes
genome Accessing/modifying sequence information
genome-method Seqinfo objects
genome-method Accessing/modifying sequence information
genome<- Accessing/modifying sequence information
genome<--method Seqinfo objects
genome<--method Accessing/modifying sequence information
GenomeDescription GenomeDescription objects
GenomeDescription-class GenomeDescription objects
genomeStyles Conveniently rename the seqlevels of an object according to a given style
intersect-method Seqinfo objects
isCircular Accessing/modifying sequence information
isCircular-method Seqinfo objects
isCircular-method Accessing/modifying sequence information
isCircular<- Accessing/modifying sequence information
isCircular<--method Seqinfo objects
isCircular<--method Accessing/modifying sequence information
keepSeqlevels Convenience wrappers to the seqlevels() getter and setter
keepStandardChromosomes Convenience wrappers to the seqlevels() getter and setter
length-method Seqinfo objects
mapSeqlevels Conveniently rename the seqlevels of an object according to a given style
merge-method Seqinfo objects
names-method Seqinfo objects
names<--method Seqinfo objects
orderSeqlevels Assign sequence IDs to sequence names
organism GenomeDescription objects
organism-method GenomeDescription objects
provider GenomeDescription objects
provider-method GenomeDescription objects
providerVersion GenomeDescription objects
providerVersion-method GenomeDescription objects
rankSeqlevels Assign sequence IDs to sequence names
releaseDate GenomeDescription objects
releaseDate-method GenomeDescription objects
releaseName GenomeDescription objects
releaseName-method GenomeDescription objects
renameSeqlevels Convenience wrappers to the seqlevels() getter and setter
restoreSeqlevels Convenience wrappers to the seqlevels() getter and setter
Seqinfo Seqinfo objects
seqinfo Accessing/modifying sequence information
Seqinfo-class Seqinfo objects
seqinfo-method GenomeDescription objects
seqinfo<- Accessing/modifying sequence information
seqlengths Accessing/modifying sequence information
seqlengths-method Seqinfo objects
seqlengths-method Accessing/modifying sequence information
seqlengths<- Accessing/modifying sequence information
seqlengths<--method Seqinfo objects
seqlengths<--method Accessing/modifying sequence information
seqlevels Accessing/modifying sequence information
seqlevels-method Seqinfo objects
seqlevels-method Accessing/modifying sequence information
seqlevels-wrappers Convenience wrappers to the seqlevels() getter and setter
seqlevels0 Accessing/modifying sequence information
seqlevels<- Accessing/modifying sequence information
seqlevels<--method Seqinfo objects
seqlevels<--method Accessing/modifying sequence information
seqlevelsInGroup Conveniently rename the seqlevels of an object according to a given style
seqlevelsInUse Accessing/modifying sequence information
seqlevelsInUse-method Accessing/modifying sequence information
seqlevelsStyle Conveniently rename the seqlevels of an object according to a given style
seqlevelsStyle-method Conveniently rename the seqlevels of an object according to a given style
seqlevelsStyle<- Conveniently rename the seqlevels of an object according to a given style
seqlevelsStyle<--method Conveniently rename the seqlevels of an object according to a given style
seqnames Accessing/modifying sequence information
seqnames-method GenomeDescription objects
seqnames-method Seqinfo objects
seqnames<- Accessing/modifying sequence information
seqnames<--method Seqinfo objects
show-method GenomeDescription objects
show-method Seqinfo objects
sortSeqlevels Accessing/modifying sequence information
sortSeqlevels-method Accessing/modifying sequence information
specData Species Mapper object and/or list of valid taxonomy Ids
species GenomeDescription objects
species-method GenomeDescription objects
speciesMap Species Mapper object and/or list of valid taxonomy Ids
summary-method Seqinfo objects
summary.Seqinfo Seqinfo objects
validTaxIds Species Mapper object and/or list of valid taxonomy Ids
[-method Seqinfo objects