[BioC] chromLocation

[James W. MacDonald]

 >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.

First, you should always state what package you are using when you ask 
about a particular function. There are something like 150 packages on 
BioC these days, and having to do a search to find that this function is 
in the ideogram package decreases the likelihood of getting an answer.

That said, this seems like a very roundabout way to get the information 
you want. It would be much easier to simply extract the data from the 
hgu133plus2 package directly.

Something like this (where probids is a vector of probe IDs)

out <- mget(probids, hgu133plus2MAP)

will give you a named list containing the cytoband positions. You could 
turn this into a named vector using unlist(out), and I suppose a matrix 
using cbind(names(out), unlist(out)) but that would be sort of weird 
because the row.names would be the probe IDs as well.

Unless you just want the output I would stick with the list; a list may 
be conceptually more difficult to work with, but once you know how to 
manipulate them you will see that they are in many ways superior to a 
matrix. Additionally, there are some probesets that are not mapped to a 
single cytoband location:

 > table(sapply(mget(ls(hgu133plus2MAP), hgu133plus2MAP),length))

     1     2     3
54643    29     3

although the three probesets that appear to be mapped to three cytoband 
locations are only mapped to two (1q43|1q23.1).

Best,

Jim

 >
 >Thanks,
 >Beth
 >
 >
 >	[[alternative HTML version deleted]]
 >

-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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