supportedSeqnameStyles {AnnotationDbi}R Documentation

List the supported seqname styles for all supported organisms

Description

Lists out the available seqname styles for all organisms supported by the seqnames.db database.

Usage

supportedSeqnameMappings()
findSequenceRenamingMaps(seqnames, style, best.only=TRUE, drop=TRUE)
supportedSeqnameStyles()
isSupportedSeqnamesStyle(style, species)
extractSeqnameSet(style, species)
listAllSupportedSeqnameStyles()
listAllSupportedStylesBySpecies(species)
supportedSeqnames()
testSeqnames(styles, seqnames, species)

Arguments

best.only

if TRUE (the default), then only the "best" sequence renaming maps (i.e. the rows with less NAs) are returned.

drop

if TRUE (the default), then a vector is returned instead of a matrix when the matrix has only 1 row.

seqnames

the seqnames. These are given as a character vector and are the labels attached to the chromosomes in a genome.

style

a character vector with a single element to specify the style.

species

The genus and species of the organism in question separated by a single space. Don't forget to capitalize the genus.

styles

same as style, but expecting a character vector which could have multiple elements.

Details

supportedSeqnameMappings: Returns the list of all supported seqname mappings, one per supported organism. Each mapping is represented as a data frame with 1 column per seqname style and 1 row per chromosome name (not all chromosomes of a given organism necessarily belong to the mapping).

findSequenceRenamingMaps: Returns a matrix with 1 column per supplied sequence name and 1 row per sequence renaming map compatible with the specified style. If best.only is TRUE (the default), only the "best" renaming maps (i.e. the rows with less NAs) are returned.

supportedSeqnameStyles: Different organizations have different naming conventions for how they name the biologically defined sequence elements (usually chromosomes) for each organism they support. The seqnames.db package contains a database that defines these different conventions. The supportedSeqnameStyles function allows users to discover which conventions are currently encoded by the seqnames DB.

isSupportedSeqnamesStyle: Returns TRUE or FALSE depending on whether or not a suspected style and species are legitimately defined in seqnames.db.

extractSeqnameSet: Extracts the seqnames for a single style and species.

listAllSupportedSeqnameStyles: Returns a list of character vectors where each character vector contains the seqnames for a particular style. This effectively dumps the whole seqnames.db DB into a single list object.

listAllSupportedStylesBySpecies: List out only the supported styles for a particular species.

supportedSeqnames: This just lists all possible seqnames for the database as a single unique character vector.

testSeqnames: Takes a character vector of styles, a set of seqnames and a species and determines for each style whether or not the seqnames given are a match. Returns a TRUE/FALSE vector of the same length as styles.

Value

A character list containing character vectors with the names of all seqname styles for each supported species. The names of the list are the species names for each supported organism.

Author(s)

Marc Carlson

Examples

  supportedSeqnameMappings()
  findSequenceRenamingMaps(c("chrII", "chrIII", "chrM"), "NCBI")
  findSequenceRenamingMaps(c("chrII", "chrIII", "chrM"), "Ensembl")

  library("TxDb.Hsapiens.UCSC.hg19.knownGene")
  txdb = TxDb.Hsapiens.UCSC.hg19.knownGene
  species = species(txdb)
  style = "NCBI"

  supportedSeqnameStyles()

  isSupportedSeqnamesStyle(style, species)

  extractSeqnameSet(style=style,species=species)

  listAllSupportedSeqnameStyles()

  supportedSeqnames()


  styles = c("NCBI","UCSC")
  seqnames = as.character(c(1:5,"Pt","Mt"))

  testSeqnames(styles, seqnames, species)

[Package AnnotationDbi version 1.22.6 Index]