Pos.gene: Find the chromosome, start and end position for gene names

Description

Allows retrieval of the the chromosome position associated with a HGNC gene label, or vector of such labels. Note that the position returned for genes is not a single point as for SNPs, so the result will be a chromosome, then a position range with start and end.

Usage

Pos.gene(genes, build = NULL, dir = NULL, bioC = FALSE, band = FALSE,
  one.to.one = TRUE, remap.extra = FALSE, discard.extra = TRUE,
  warnings = TRUE)

Arguments

genes

character, a vector of gene ids

build

character, "hg18" or "hg19" (or 36/37) to show which reference to retrieve. The default when build is NULL is to use the build from the current ChipInfo annotation

dir

character, 'dir' is the location to download gene annotation information to; 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.

bioC

logical, if true then return position information as a GRanges object, else a data.frame

band

logical, whether to include band/stripe in returned object

one.to.one

logical, some genes have split ranges, TRUE merges these to give only 1 range per gene, NB: this is the default behaviour when using the more general Pos() function

remap.extra

logical, if TRUE genes with chromosome annotation 'c6_cox' and 'c6_QBL' will be mapped to chromosome 6, and 'NT_xxxx' chromosome labels will all be mapped to 'Z_NT', etc

discard.extra

logical, if TRUE then any gene hit with chromosome not in 1:22, X, Y, XY, MT, will be discarded.

warnings

logical, whether to show warnings when some/all ids are not matched to the reference

Value

Returns a data.frame with columns 'chr' [chromosome], 'start' [starting position of the gene],'end' [end position of the gene], or if bioC=TRUE, then returns a GRanges object with equivalent information, and if band=TRUE, then an extra column is added with band information If returning a data.frame, then it will be in the same order as 'genes'. If bioC=TRUE, then the result will be in genome order, regardless of the order of 'genes'.

Examples

Run this code

# NOT RUN {
setwd(tempdir())
Pos.gene(c("CTLA4","PTPN22"))
Pos.gene("MYC",build=36)
Pos.gene("MYC",build=37)
Pos.gene(c("CTLA4","PTPN22"),bioC=TRUE,band=TRUE)
Pos.gene(c("CTLA4","OR2A1"),one.to.one=TRUE,build=38) # OR2A1 is split over two ranges
Pos.gene(c("CTLA4","OR2A1"),one.to.one=FALSE,build=38)
Pos.gene("RNU2-1",one.to.one=FALSE,bioC=TRUE,build=38) # RNU2-1 is split over multiple ranges
# }

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