R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 8 of 8 found.
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available.species (Package: GenomeInfoDb) :

NCBI maintains a collection of unique taxonomy Ids and pairs these with associated genus and species designations. This function returns the set of pre-processed values that we use to check that something is a valid Taxonomy ID (or species name)

● Data Source: BioConductor
● Keywords: manip
● Alias: available.species
● 0 images

fetchExtendedChromInfoFromUCSC (Package: GenomeInfoDb) :

Fetch the chromosomes info for some UCSC genomes. Only supports hg38, hg19, hg18, panTro4, panTro3, panTro2, bosTau8, bosTau7, bosTau6, canFam3, canFam2, canFam1, musFur1, mm10, mm9, mm8, susScr3, susScr2, rn6, rheMac3, rheMac2, galGal4, galGal3, gasAcu1, danRer7, apiMel2, dm6, dm3, ce10, ce6, ce4, ce2, sacCer3, and sacCer2 at the moment.

● Data Source: BioConductor
● Keywords: manip
● Alias: fetchExtendedChromInfoFromUCSC
● 0 images

rankSeqlevels (Package: GenomeInfoDb) : Assign sequence IDs to sequence names

rankSeqlevels assigns a unique ID to each unique sequence name in the input vector. The returned IDs span 1:N where N is the number of unique sequence names in the input vector.

● Data Source: BioConductor
● Keywords: manip
● Alias: orderSeqlevels, rankSeqlevels
● 0 images

seqinfo (Package: GenomeInfoDb) : Accessing/modifying sequence information

A set of generic functions for getting/setting/modifying the sequence information stored in an object.

● Data Source: BioConductor
● Keywords: methods
● Alias: genome, genome,ANY-method, genome<-, genome<-,ANY-method, isCircular, isCircular,ANY-method, isCircular<-, isCircular<-,ANY-method, seqinfo, seqinfo<-, seqlengths, seqlengths,ANY-method, seqlengths<-, seqlengths<-,ANY-method, seqlevels, seqlevels,ANY-method, seqlevels0, seqlevels<-, seqlevels<-,ANY-method, seqlevelsInUse, seqlevelsInUse,CompressedList-method, seqlevelsInUse,Vector-method, seqnames, seqnames<-, sortSeqlevels, sortSeqlevels,ANY-method, sortSeqlevels,character-method
● 0 images

seqlevels-wrappers (Package: GenomeInfoDb) :

Keep, drop or rename seqlevels in objects with a Seqinfo class.

● Data Source: BioConductor
● Keywords: methods, utilities
● Alias: seqlevels-wrappers
● 0 images

seqlevelsStyle (Package: GenomeInfoDb) :

The seqlevelsStyle getter and setter can be used to get the current seqlevels style of an object and to rename its seqlevels according to a given style.

● Data Source: BioConductor
● Keywords:
● Alias: seqlevelsStyle, seqlevelsStyle,ANY-method, seqlevelsStyle,character-method, seqlevelsStyle<-, seqlevelsStyle<-,ANY-method, seqlevelsStyle<-,character-method
● 0 images

GenomeDescription-class (Package: GenomeInfoDb) : GenomeDescription objects

A GenomeDescription object holds the meta information describing a given genome.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: GenomeDescription, GenomeDescription-class, class:GenomeDescription
● 0 images

Seqinfo-class (Package: GenomeInfoDb) : Seqinfo objects

A Seqinfo object is a table-like object that contains basic information about a set of genomic sequences. The table has 1 row per sequence and 1 column per sequence attribute. Currently the only attributes are the length, circularity flag, and genome provenance (e.g. hg19) of the sequence, but more attributes might be added in the future as the need arises.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: Seqinfo, Seqinfo-class, class:Seqinfo
● 0 images