Question: Example of gene2cat goseq
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gravatar for Biogeek
9 days ago by
Biogeek350
Biogeek350 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.

Thanks.

goseq • 88 views
ADD COMMENTlink modified 9 days ago by cfos4698130 • written 9 days ago by Biogeek350

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 9 days ago by RamRS21k
0
gravatar for cfos4698
9 days ago by
cfos4698130
cfos4698130 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 runGOseq.pl 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 9 days ago by cfos4698130
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