[BioC] chromLocation

Furge, Kyle Kyle.Furge at vai.org
Mon Jan 9 16:43:02 CET 2006

A complication is that the chrObj.band contains information for not only
which genes map to each chromosome, but also which genes map to each band.
In addition, the object holds chromosome location information as well.

A mentioned earlier it may be easier to get this information from the
annotation environment directly (i.e. using mget() or contents() from the
hgu133plus2MAP environment)

However, this code will construct the desired matrix using chrObj.band

## get the chromLoc object that holds just band information
cL <- chrObj.bands at chromLocs
ix <- which(names(cL) %in% cL$bandList)
cL <- cL[ix]

## Extract the data
probe <- c()
band <- c()
for(i in 1:length(cL)) {
  p <- names(cL[[i]])
  probe <- c(probe,p)
  band <- c(band,rep(names(cL)[i],length(p)))

## make a matrix
m <- cbind(probe,band)


> From: "Beth Wilmot" <wilmotb at ohsu.edu>
> Date: Fri, 06 Jan 2006 19:27:45 -0800
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] chromLocation
> Hello,
> I have created a chromLocation object by:
> chrObj.bands<-buildChromLocation.2("hgu133plus2",major=c("arms","bands")
> I have a list of probe IDs for which I would like only the cytoband
> information. I am having trouble separating the genome position from the probe
> id and then matching the probe id to the cytoband information.  I would like a
> matrix:
> Probe Id     cytoband
> xxxxx           xxxxx
> Any help would be appreciated.
> Thanks,
> Beth
> [[alternative HTML version deleted]]
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