Description Usage Arguments Value Author(s) See Also Examples
Allows retrieval of cytobands/karyotypes intersected by a chromosome and position, which can be entered using chr, pos/start/end vectors, or a RangedData or GRanges object
1 2 |
chr |
character, an optional vector of chromosomes to combine with 'pos' or 'start'+'end' (enter in ...) to describe positions to retrieve the possible overlapping cytoband(s) |
pos |
integer, an optional vector of chromosome positions (for SNPs), no need to enter start or end if this is entered, and vice-versa |
start |
integer, an optional vector of start points for chromosome ranges |
end |
integer, an optional vector of end points for chromosome ranges |
ranges |
optional GRanges or RangedData object describing positions for which we want bands, removing the need to enter chr, pos, start or end |
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, or RangedData if 'ranges' is RangedData, else a data.frame |
one.to.one |
logical, whether to concatenate multiple hits for the same range into one result, or spread the result over multiple lines, one for each cytoband overlapped |
Returns a set of cytobands separated by semicolons (if more than one) for each range entered. If bioC=TRUE, returns the equivalent as a GRanges object, unless a RangedData object was used for the ranges parameter, in which case a RangedData object would be returned. If one.to.one is FALSE, then instead of concatenating multiple cytobands into one line per range, each is listed separately as a new row, with an index added to correspond to the original input order of ranges, if bioC=TRUE; or just adds additional elements to the resulting vector if bioC=FALSE.
Nicholas Cooper nick.cooper@cimr.cam.ac.uk
Chr
, Pos
, Pos.band
, Band
,
Band.gene
, Band.pos
, Gene.pos
1 2 3 4 5 6 7 8 | setwd(tempdir())
Band.pos(chr=6, start=31459636, end=31462760)
Band.pos(chr=22, pos=3452345)
Band.pos(Chr("rs689"),Pos("rs689")) # combine Chr(), Pos() to find the cytoband for SNP rs689
Band.pos(chr=1,start=110000000,end=120000000,build="hg19") # multiple cytobands in range
Band.pos(chr=1,start=110000000,end=120000000,one.to.one=FALSE) # list separately
Band.pos(Pos.band(c("13q21.31","1p13.2"),bioC=TRUE)) # use ranges object returned by Pos.band()
# note that 3 ranges are returned for each entry as the start/end overlap the adjacent ranges
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