Change naming style for a set of sequence names

If available, use the information from GenomeInfoDb for your species of interest to map the sequence names from the style currently used to another valid style. For example, for Homo sapiens map '2' (NCBI style) to 'chr2' (UCSC style). If the information from GenomeInfoDb is not available, the original sequence names will be returned. To disable this functionality specify set chrsStyle to NULL.

extendedMapSeqlevels(
  seqnames,
  style = getOption("chrsStyle", "UCSC"),
  species = getOption("species", "homo_sapiens"),
  currentStyle = NULL,
  ...
)

Arguments

seqnames

A character vector with the sequence names.

style

A single character vector specifying the naming style to use for renaming the sequence names.

species

A single character vector with the species of interest: it has to match the valid species names supported in GenomeInfoDb. See names(GenomeInfoDb::genomeStyles()). If species = NULL, a guess will be made using the available information in GenomeInfoDb.

currentStyle

A single character vector with the currently used naming style. If NULL, a guess will be made from the naming styles supported by species.

...

Arguments passed to other methods and/or advanced arguments. Advanced arguments:

verbose

If TRUE basic status updates will be printed along the way.

chrsStyle

The naming style of the chromosomes. By default, UCSC. See seqlevelsStyle. Set to NULL to disable this function. This is used when style is missing, which is normally the case when extendedMapSeqlevels is called by other functions.

Value

A vector of sequence names using the specified naming style.

Details

This function is inspired from mapSeqlevels with the difference that it will return the original sequence names if the species, current naming style or target naming style are not supported in GenomeInfoDb.

If you want to disable this function, set chrsStyle to NULL. From other functions in derfinder that pass the ... argument to this function, use chrsStyle = NULL. This can be useful when working with organisms that are absent from GenomeInfoDb as documented in https://support.bioconductor.org/p/95521/.

Author

L. Collado-Torres

Examples

## Without guessing any information
extendedMapSeqlevels("2", "UCSC", "Homo sapiens", "NCBI")
#> [1] "chr2"

## Guessing the current naming style
extendedMapSeqlevels("2", "UCSC", "Homo sapiens")
#> extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens
#> [1] "chr2"

## Guess species and current style
extendedMapSeqlevels("2", "NCBI")
#> [1] "2"

## Guess species while supplying the current style.
## Probably an uncommon use-case
extendedMapSeqlevels("2", "NCBI", currentStyle = "TAIR10")
#> extendedMapSeqlevels: the 'currentStyle' TAIR10 is currently not supported for the 'species' homo_sapiens in GenomeInfoDb. Check valid naming styles by running GenomeInfoDb::genomeStyles(species). If it's not present, consider adding your genome by following the information at http://www.bioconductor.org/packages/release/bioc/vignettes/GenomeInfoDb/inst/doc/Accept-organism-for-GenomeInfoDb.pdf
#> [1] "2"

## Sequence names are unchanged when using an unsupported species
extendedMapSeqlevels("seq2", "NCBI", "toyOrganism")
#> extendedMapSeqlevels: the 'seqnames' you supplied are currently not supported in GenomeInfoDb. Consider adding your genome by following the information at http://www.bioconductor.org/packages/release/bioc/vignettes/GenomeInfoDb/inst/doc/Accept-organism-for-GenomeInfoDb.pdf
#> [1] "seq2"

## Disable extendedMapSeqlevels. This can be useful when working with
## organisms that are not supported by GenomeInfoDb
chrs <- c(
    "I", "II", "III", "IV", "IX", "V", "VI", "VII", "VIII", "X",
    "XI", "XII", "XIII", "XIV", "XV", "XVI", "XVII"
)
extendedMapSeqlevels(chrs, chrsStyle = NULL)
#>  [1] "I"    "II"   "III"  "IV"   "IX"   "V"    "VI"   "VII"  "VIII" "X"   
#> [11] "XI"   "XII"  "XIII" "XIV"  "XV"   "XVI"  "XVII"
if (FALSE) {
## Set global species and style option
options("chrsStyle" = "UCSC")
options("species" = "homo_sapiens")

## Run using global options
extendedMapSeqlevels("2")
}