Pos.band: Find the chromosome, start and end position for cytoband...

In humarray: Simplify Analysis and Annotation of Human Microarray Datasets

Description

Allows retrieval of the the chromosome position of a karyotype/cytoband label, or vector of such labels. Note that the position returned for bands is not a single point as for SNPs, so the result will be a chromosome, then a position range with start and end, and lastly the band without the chromosome prefix

Usage

Pos.band(bands, build = NULL, dir = NULL, bioC = FALSE)

Arguments

bands	character, a vector of cytoband labels, chromosome[p/q]xx.xx ; e.g, 13q21.31, Yq11.221, 6p23, etc
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 cyto annotation 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.
bioC	logical, if true then return position information as a GRanges object, else a data.frame

Value

Returns a data.frame with columns 'chr' [chromosome], 'start' [starting position of the gene],'end' [end position of the gene] and 'band' [band without the chromosome prefix], or if bioC=TRUE, then returns a GRanges object with equivalent information. If returning a data.frame, then it will be in the same order as 'bands'. If bioC=TRUE, then the result will be in genome order, regardless of the order of 'bands'.

Author(s)

Nicholas Cooper [e-mail]

See Also

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

Examples

setwd(tempdir())
Pos.band("1p13.2")
Pos.band("Yq11.221",build=36)
Pos.band("Yq11.221",build=37)
Pos.band(c("13q21.31","1p13.2","2q33.2","6p23"),bioC=TRUE)

humarray documentation built on Nov. 20, 2017, 1:05 a.m.