Pos.band: Find the chromosome, start and end position for cytoband names
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'.
# NOT RUN {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)
# }