Question: Example of gene2cat goseq
gravatar for Biogeek
10 months ago by
Biogeek380 wrote:

Any examples of the gene2cat input for a non-model organism? I'm working in R. My first column is GO:XXXXXX and my second column is gene ID. Row names are numerical (automatic). To be fair the Vignette and guides aren't so clear considering a lot of people use it for non-model organisms.

I'm getting the error:

Was expecting a dataframe or a list mapping categories to genes.  Check gene2cat input and try again.

I'm using a dataframe.


goseq • 390 views
ADD COMMENTlink modified 10 months ago by cfos4698140 • written 10 months ago by Biogeek380

Please use something like reprex to show us the first few lines of your data frame as well as the exact code you're running.

ADD REPLYlink written 10 months ago by RamRS25k
gravatar for cfos4698
10 months ago by
cfos4698140 wrote:

I'm currently using GOseq at the moment, and am having some success using helper scripts with Trinity software. As the Trinity developers note, the scripts are intended as a basic guide and customization for your own data set might be necessary.

Anyway, the bundled script generates another R script to run GOseq on each DE contrast of interest. Following each step of the script generates an object for the gene2cat argument called "GO_info_listed". This object is a list of lists. Each list contains all GO terms associated with a particular gene. For example, GO_info_listed$GeneX might have 15 elements, each of which is a particular GO term.

This list of lists might sound difficult to generate, but if you follow the Trinity website and the script, you should get there.

ADD COMMENTlink written 10 months ago by cfos4698140
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