GenomeInfoDb (version 1.2.4)

seqlevelsStyle: Conveniently rename the seqlevels of an object according to a given style

Description

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.

Usage

seqlevelsStyle(x)
seqlevelsStyle(x) <- value
## Related low-level utilities:
genomeStyles(species)
extractSeqlevels(species, style)
extractSeqlevelsByGroup(species, style, group)
mapSeqlevels(seqnames, style, best.only=TRUE, drop=TRUE)
seqlevelsInGroup(seqnames, group, species, style)

Arguments

x

The object from/on which to get/set the seqlevels style.

value

A single character string that sets the seqnameStyle for x.

species

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

style

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

group

Group can be 'auto' for autosomes, 'sex' for sex chromosomes/allosomes, 'circular' for circular chromosomes. The default is 'all' which returns all the chromosomes.

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

a character vector containing the labels attached to the chromosomes in a given genome for a given style. For example : For Homo sapiens, NCBI style - they are "1","2","3",...,"X","Y","MT"

Value

For seqlevelsStyle returns a single character string containing the style of the seqlevels supplied. Note that this information is not stored in x but inferred by looking up a seqlevels style database stored inside GenomeInfoDb.For extractSeqlevels , extractSeqlevelsByGroup and seqlevelsInGroup returns a character vector of seqlevels for given supported species and group.For mapSeqlevels returns a matrix with 1 column per supplied sequence name and 1 row per sequence renaming map compatible with the specified styleFor genomeStyle : If species is specified returns a data.frame containg the seqlevels style and its mapping for a given organism. If species is not specified, a list is returned with one list per species containing the seqlevels style with the corresponding mappings.

Details

seqlevelsStyle(x), seqlevelsStyle(x) <- value: Get the current seqlevels style of an object, or rename its seqlevels according to the supplied style.

genomeStyles: Different organizations have different naming conventions for how they name the biologically defined sequence elements (usually chromosomes) for each organism they support. The Seqnames package contains a database that defines these different conventions. genomeStyles() 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). genomeStyles(species) returns a data.frame only for the given organism with all its supported seqname mappings. extractSeqlevels: Returns a character vector of the seqnames for a single style and species. extractSeqlevelsByGroup: Returns a character vector of the seqnames for a single style and species by group. Group can be 'auto' for autosomes, 'sex' for sex chromosomes/ allosomes, 'circular' for circular chromosomes. The default is 'all' which returns all the chromosomes. mapSeqlevels: 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. seqlevelsInGroup: It takes a character vector along with a group and optional style and species.If group is not specified , it returns "all" or standard/top level seqnames. Returns a character vector of seqnames after subsetting for the group specified by the user. See examples for more details.

Examples

## ---------------------------------------------------------------------
## seqlevelsStyle() getter and setter
## ---------------------------------------------------------------------

## find the seqname Style for a given character vector 
seqlevelsStyle(paste0("chr", 1:30))

## Rename the seqlevels of a GRanges object with the seqlevelsStyle()
## setter:
library(GenomicRanges)
gr <- GRanges(rep(c("chr2", "chr3", "chrM"), 2), IRanges(1:6, 10))

seqlevelsStyle(gr)
seqlevelsStyle(gr) <- "NCBI"
gr

seqlevelsStyle(gr)
seqlevelsStyle(gr) <- "dbSNP"
gr

seqlevelsStyle(gr)
seqlevelsStyle(gr) <- "UCSC"
gr

## ---------------------------------------------------------------------
## Related low-level utilities
## ---------------------------------------------------------------------

names(genomeStyles())
genomeStyles("Homo_sapiens")
"UCSC" %in% names(genomeStyles("Homo_sapiens"))

## List the supported seqname style for the given species and the given
## style
extractSeqlevels(species="Drosophila_melanogaster" , style="Ensembl")

## List all sex chromosomes for Homo sapiens using style UCSC
## 3 groups are supported: 'auto' for autosomes, 'sex' for allosomes 
## and 'circular' for circular chromosomes  
extractSeqlevelsByGroup(species="Homo_sapiens", style="UCSC", group="sex")

## find whether the seqnames belong to a given group
newchr <- paste0("chr",c(1:22,"X","Y","M","1_gl000192_random","4_ctg9"))
seqlevelsInGroup(newchr, group="sex")

newchr <- as.character(c(1:22,"X","Y","MT"))
seqlevelsInGroup(newchr, group="all","Homo_sapiens","NCBI")

## if we have a vector conatining seqnames and we want to verify the
## species and style for them , we can use:
seqnames <- c("chr1","chr9", "chr2", "chr3", "chr10")
all(seqnames %in% extractSeqlevels("Homo_sapiens", "UCSC"))

## find mapped seqlevelsStyles for exsiting seqnames
mapSeqlevels(c("chrII", "chrIII", "chrM"), "NCBI")
mapSeqlevels(c("chrII", "chrIII", "chrM"), "Ensembl")