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

In GenomeInfoDb: Utilities for manipulating chromosome names, including modifying them to follow a particular naming 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. x must have a seqlevels method or be a character vector.
value	A single character string that sets the seqlevels style 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"

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.

Value

For seqlevelsStyle: A single string containing the style of the seqlevels in x, or a character vector containing the styles of the seqlevels in x if the current style cannot be determined unambiguously. Note that this information is not stored in x but inferred from its seqlevels using a heuristic helped by a seqlevels style database stored in the GenomeInfoDb package. If the underlying genome is known (i.e. if unique(genome(x)) is not NA), the name of the genome or assembly (e.g. ce11 or WBcel235) is also used by the heuristic.

For extractSeqlevels , extractSeqlevelsByGroup and seqlevelsInGroup: A character vector of seqlevels for given supported species and group.

For mapSeqlevels: A matrix with 1 column per supplied sequence name and 1 row per sequence renaming map compatible with the specified style.

For 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.

Author(s)

Sonali Arora, Martin Morgan, Marc Carlson, H. Pagès

Examples

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

## On a character vector:
x <- paste0("chr", 1:5)
seqlevelsStyle(x)
seqlevelsStyle(x) <- "NCBI"
x

## On a GRanges object:
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

## In general the seqlevelsStyle() setter doesn't know how to rename
## scaffolds. However, if the genome is specified, it's very likely
## that seqlevelsStyle() will be able to take advantage of that:
gr <- GRanges(rep(c("2", "Y", "Hs6_111610_36"), 2), IRanges(1:6, 10))
genome(gr) <- "NCBI36"
seqlevelsStyle(gr) <- "UCSC"
gr

## On a Seqinfo object:
si <- si0 <- Seqinfo(genome="apiMel2")
si
seqlevelsStyle(si) <- "NCBI"
si
seqlevelsStyle(si) <- "RefSeq"
si
seqlevelsStyle(si) <- "UCSC"
stopifnot(identical(si0, si))

si <- si0 <- Seqinfo(genome="WBcel235")
si
seqlevelsStyle(si) <- "UCSC"
si
seqlevelsStyle(si) <- "RefSeq"
si
seqlevelsStyle(si) <- "NCBI"
stopifnot(identical(si0, si))

si <- Seqinfo(genome="macFas5")
si
seqlevelsStyle(si) <- "NCBI"
si

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

## Genome styles:
names(genomeStyles())
genomeStyles("Homo_sapiens")
"UCSC" %in% names(genomeStyles("Homo_sapiens"))

## Extract seqlevels based on species, style and group:
## The 'group' argument can be 'sex', 'auto', 'circular' or 'all'.

## All:
extractSeqlevels(species="Drosophila_melanogaster", style="Ensembl")

## Sex chromosomes:
extractSeqlevelsByGroup(species="Homo_sapiens", style="UCSC", group="sex")

## Autosomes:
extractSeqlevelsByGroup(species="Homo_sapiens", style="UCSC", group="auto")


## Identify which seqnames belong to a particular '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")

## Identify which seqnames belong to a species and style:
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")

GenomeInfoDb documentation built on April 9, 2021, 6 p.m.