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\name{GenomeInfoDb-helpers}
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\alias{GenomeInfoDb-helpers}
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\alias{extractSeqlevels}
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\alias{extractSeqlevelsByGroup}
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\alias{seqlevelsInGroup}
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\alias{seqlevelsStyle}
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\alias{seqlevelsStyle,character-method}
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\alias{seqlevelsStyle<-}
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\alias{seqlevelsStyle<-,character-method}
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List the supported seqname styles for all supported organisms
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List the supported seqname styles for all supported organisms
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extractSeqlevels(species, style)
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extractSeqlevelsByGroup(species, style, group)
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orderSeqlevels(seqnames, X.is.sexchrom = NA)
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mapSeqlevels(seqnames, style, best.only=TRUE, drop=TRUE)
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seqlevelsInGroup(seqnames, group, species, style)
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seqlevelsStyle(x) <- value
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The genus and species of the organism in question
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separated by a single space. Don't forget to capitalize the genus.}
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a character vector with a single element to specify the style.}
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Group can be 'auto' for autosomes, 'sex' for
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sex chromosomes/allosomes, 'circular' for circular chromosomes. The
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default is 'all' which returns all the chromosomes.}
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if \code{TRUE} (the default), then only the "best"
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sequence renaming maps (i.e. the rows with less NAs) are returned.}
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if \code{TRUE} (the default), then a vector is returned
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instead of a matrix when the matrix has only 1 row.}
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a character vector containing the labels attached to the
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chromosomes in a given genome for a given style. For example : For
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\emph{Homo sapiens}, NCBI style - they are
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"1","2","3",...,"X","Y","MT"}
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A logical indicating whether X refers to the sexual chromosome or
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to chromosome with Roman Numeral X. If \code{NA},
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\code{makeSeqnameIds} does its best to "guess".
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The object from/on which to get/set the sequence information.}
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A single character string that sets the seqnameStyle for \code{x}.}
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For \code{extractSeqlevels} , \code{extractSeqlevelsByGroup} and
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\code{seqlevelsInGroup} returns a character vector of seqlevels
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for given supported species and group.
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For \code{mapSeqlevels} returns a matrix with 1 column per supplied sequence
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name and 1 row per sequence renaming map compatible with the specified style
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For \code{seqlevelsStyle} returns a single character string containing the
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style of the seqlevels supplied. Note that this information is not stored in
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\code{x} but inferred by looking up a seqlevel style database stored inside
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For \code{genomeStyle} : If species is specified returns a data.frame
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containg the seqlevel style and its mapping for a given organism. If species
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is not specified, a list is returned with one list per species containing
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the seqlevel style with the corresponding mappings.
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For \code{orderSeqlevels} returns an integer vector with indices of seqlevels
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in their natural order.
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Different organizations have different naming conventions for how they
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name the biologically defined sequence elements (usually chromosomes)
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for each organism they support. The Seqnames package contains a
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database that defines these different conventions.
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genomeStyles() returns the list of all supported seqname mappings,
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one per supported organism. Each mapping is represented as a data frame
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with 1 column per seqname style and 1 row per chromosome name
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(not all chromosomes of a given organism necessarily belong to the mapping).
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genomeStyles(species) returns a data.frame only for the given organism
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with all its supported seqname mappings.
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\code{extractSeqlevels}:
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Returns a character vector of the seqnames for a single style and species.
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\code{extractSeqlevelsByGroup}:
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Returns a character vector of the seqnames for a single style and species
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by group. Group can be 'auto' for autosomes, 'sex' for sex chromosomes/
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allosomes, 'circular' for circular chromosomes. The default is 'all' which
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returns all the chromosomes.
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\code{orderSeqlevels}:
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Returns an integer vector while attempting to provide the \dQuote{natural}
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order of seqnames, e.g.,\code{chr1}, \code{chr2}, \code{chr3}, \ldots
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Returns a matrix with 1 column per supplied sequence name and 1 row
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per sequence renaming map compatible with the specified style.
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If \code{best.only} is \code{TRUE} (the default), only the "best"
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renaming maps (i.e. the rows with less NAs) are returned.
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\code{seqlevelsInGroup}:
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It takes a character vector along with a group and optional style and
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species.If group is not specified , it returns "all" or standard/top level
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Returns a character vector of seqnames after subsetting for the group
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specified by the user. See examples for more details.
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\code{seqlevelsStyle(x)}: finds the seqlevelsStyle for a given character
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Sonali Arora \email{sarora@fhcrc.org}, Martin Morgan , Marc Carlson,
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names(genomeStyles())
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genomeStyles("Homo_sapiens")
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"UCSC" \%in\% names(genomeStyles("Homo_sapiens"))
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## List the supported seqname style for the given species and the given
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extractSeqlevels(species="Drosophila_melanogaster" , style="Ensembl")
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## List all sex chromosomes for Homo sapiens using style UCSC
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## 3 groups are supported: 'auto' for autosomes, 'sex' for allosomes
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## and 'circular' for circular chromosomes
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extractSeqlevelsByGroup(species="Homo_sapiens", style="UCSC", group="sex")
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## find whether the seqnames belong to a given group
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newchr <- paste0("chr",c(1:22,"X","Y","M","1_gl000192_random","4_ctg9"))
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seqlevelsInGroup(newchr, group="sex")
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newchr <- as.character(c(1:22,"X","Y","MT"))
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seqlevelsInGroup(newchr, group="all","Homo_sapiens","NCBI")
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## find the seqname Style for a given character vector
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seqlevelsStyle(paste0("chr",c(1:30)))
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## order a character vector of seqnames
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seqnames <- c("chr1","chr9", "chr2", "chr3", "chr10")
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seqnames[orderSeqlevels(seqnames)]
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## if we have a vector conatining seqnames and we want to verify the
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## species and style for them , we can use:
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all(seqnames \%in\% extractSeqlevels("Homo_sapiens", "UCSC"))
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## find mapped seqlevelsStyles for exsiting seqnames
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mapSeqlevels(c("chrII", "chrIII", "chrM"), "NCBI")
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mapSeqlevels(c("chrII", "chrIII", "chrM"), "Ensembl")
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man/GenomeInfoDb-helpers.Rd
