| seqlevelsStyle {GenomeInfoDb} | R Documentation |
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.
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)
x |
The object from/on which to get/set the seqlevels style. |
value |
A single character string that sets the seqlevels style for |
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 |
drop |
if |
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" |
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.
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 by looking up a seqlevels style database stored inside the
GenomeInfoDb package.
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.
Sonali Arora, Martin Morgan, Marc Carlson, H. Pagès
## ---------------------------------------------------------------------
## seqlevelsStyle() getter and setter
## ---------------------------------------------------------------------
## character vectors:
x <- paste0("chr", 1:5)
seqlevelsStyle(x)
seqlevelsStyle(x) <- "NCBI"
x
## GRanges:
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
## ---------------------------------------------------------------------
## 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")