Question: chromLocation
gravatar for James W. MacDonald
13.9 years ago by
United States
James W. MacDonald52k wrote:
>Hello, > >I have created a chromLocation object by: > >chrObj.bands<-buildChromLocation.2("hgu133plus2",major=c("arms","ban ds") > >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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
microarray probe ideogram • 418 views
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