supportedSeqnameStyles {AnnotationDbi} | R Documentation |
Lists out the available seqname styles for all organisms supported by the seqnames.db database.
supportedSeqnameMappings() findSequenceRenamingMaps(seqnames, style, best.only=TRUE, drop=TRUE) supportedSeqnameStyles() isSupportedSeqnamesStyle(style, species) extractSeqnameSet(style, species) listAllSupportedSeqnameStyles() listAllSupportedStylesBySpecies(species) supportedSeqnames() testSeqnames(styles, seqnames, species)
best.only |
if |
drop |
if |
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. |
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.
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.
Marc Carlson
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)