Search
Question: GOHyperG function with ath1121501
0
gravatar for Thomas Girke
12.5 years ago by
Thomas Girke1.6k
United States
Thomas Girke1.6k wrote:
I have a question regarding GOHyperG function in GOstat. Is it possible to use this function with the Arabidopsis ath1121501 annotation package? The function GOHyperG requires a vector of LocusLink identifiers, however LocusLink identifiers don't seem to be available in the latest ath1121501 package since it is based on data sources from the Tair project (which is a good choice). Is there a way to work around this limitation and use this annotation package with GOHyperG? I have tried to use alternative loci identifiers, but this resulted in the below error message. Here is an example of what I have tried to do: > library(GOstats) > library(ath1121501) > library(GO) > zz1<-as.list(ath1121501ACCNUM) # or any other available mapping > zz2<-unique(unlist(zz1))[1:100] > xx<-GOHyperG(zz2, lib="ath1121501", what="MF") Error in get(x, envir, mode, inherits) : variable "ath1121501LOCUSID" of mode "environment" was not found Error in as.list(getDataEnv("LOCUSID", lib)) : unable to find the argument 'x' in selecting a method for function 'as.list' Thanks, Thomas -- Thomas Girke University of California Riverside, CA 92521
ADD COMMENTlink modified 12.5 years ago by rgentleman5.5k • written 12.5 years ago by Thomas Girke1.6k
0
gravatar for rgentleman
12.5 years ago by
rgentleman5.5k
United States
rgentleman5.5k wrote:
Hi, Not easily. Basically the current mapping is from Entrez Gene IDs to GO. So if you have a different system for going to GO categories you would need to modify the code accordingly. That is sort of the essential piece - how do you go from your IDs to GO categories, after that it is just hypergeometric calculations. Best wishes, Robert Thomas Girke wrote: > I have a question regarding GOHyperG function in GOstat. Is it > possible to use this function with the Arabidopsis ath1121501 > annotation package? The function GOHyperG requires a vector of > LocusLink identifiers, however LocusLink identifiers don't seem to be > available in the latest ath1121501 package since it is based on > data sources from the Tair project (which is a good choice). > Is there a way to work around this limitation and use this annotation > package with GOHyperG? > > I have tried to use alternative loci identifiers, but this resulted > in the below error message. Here is an example of what I have tried to do: > > >>library(GOstats) >>library(ath1121501) >>library(GO) >>zz1<-as.list(ath1121501ACCNUM) # or any other available mapping >>zz2<-unique(unlist(zz1))[1:100] >>xx<-GOHyperG(zz2, lib="ath1121501", what="MF") > > > Error in get(x, envir, mode, inherits) : variable "ath1121501LOCUSID" of mode "environment" was not found > Error in as.list(getDataEnv("LOCUSID", lib)) : > unable to find the argument 'x' in selecting a method for function 'as.list' > > Thanks, > > Thomas >
ADD COMMENTlink written 12.5 years ago by rgentleman5.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 262 users visited in the last hour