humarray (version 1.2)

Chr: Find chromosome for SNP ids, gene name or band

Description

Allows retrieval of the chromosome associated with a SNP-id, HGNC gene label, karyotype band, or vector of such ids. For SNPs the ids can be either chip ids, or rs-ids, but must be contained in the current annotation. Default behaviour is to assume 'id' are SNP ids, but if none are found in the SNP annotation, the id's will be passed to functions Pos.gene() and Pos.band() to see whether a result is found. This latter step will only happen if no SNP ids are retreived in the first instance, and if snps.only=TRUE, then genes and bands will not be searched and NA's returned. If you are repeatedly searching for chromosomes for genes/bands, using the dedicated Pos.gene and Pos.band functions would be slightly faster than relying on the fallback behaviour of the Chr() function. See documentation for these functions for more information. The build used will be that in the current ChipInfo object.

Usage

Chr(ids, dir = NULL, snps.only = FALSE)

Arguments

ids

character, a vector of rs-ids or chip-ids representing SNPs in the current ChipInfo annotation, or gene ids, or karyotype bands. Can also be a SnpMatrix object.

dir

character, only relevant when gene or band ids are entered, in this case 'dir' is the location to download gene and cytoband information; if left as NULL, depending on the value of getOption("save.annot.in.current"), the annotation will either be saved in the working directory to speed-up subsequent lookups, or deleted after use.

snps.only

logical, if TRUE, only search SNP ids, ignore the possibility of genes/cytobands.

Value

A character vector of Chromosomes for each ids, with NA values where no result was found.

See Also

Pos

Examples

# NOT RUN {
setwd(tempdir())
Chr(c("rs689","rs9467354","rs61733845"))
Chr("CTLA4")
Chr("13q21.31")
Chr(c("CTLA4","PTPN22"),snps.only=TRUE) # fails as these are genes
Chr(c("rs689","PTPN22","13q21.31")) # mixed input, will default to SNPs, as at least 1 was found
# }