Example of gene2cat goseq

Question

[Biogeek]

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.

[Ram]

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.

Answer 1

[cfos4698]

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.

[Cristina Zamora]

Thanks for your advice. Could you provide a link to follow the script of the Trinity website? I need to generate the list of lists you mentioned and I can't find it. Thank you!

[cfos4698]

Hi. You need to download and install Trinity (https://github.com/trinityrnaseq/trinityrnaseq/releases). Then, you'll find the support scripts at the following path: ${TRINITY_HOME}/Analysis/DifferentialExpression/run_GOseq.pl

There isn't necessarily a link that explains how the script works line-by-line, but the usage options for the perl script are here: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-GOSeq. I'm much better with R, so after running the perl script (with example data) I read through the R script to figure out what's going on. Good luck!