Pos.gene: Find the chromosome, start and end position for gene names
In humarray: Simplify Analysis and Annotation of Human Microarray Datasets

Description Usage Arguments Value Author(s) See Also Examples

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.

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

`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

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'.

Nicholas Cooper nick.cooper@cimr.cam.ac.uk

Chr, Pos, Pos.band, Band, Band.gene, Band.pos, Gene.pos

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