Question: Example of gene2cat goseq
1
gravatar for Biogeek
14 months ago by
Biogeek400
Biogeek400 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 • 542 views
ADD COMMENTlink modified 14 months ago by cfos4698170 • written 14 months ago by Biogeek400

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 14 months ago by RamRS27k
1
gravatar for cfos4698
14 months ago by
cfos4698170
cfos4698170 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 14 months ago by cfos4698170

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!

ADD REPLYlink written 29 days ago by Cristina Zamora0

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!

ADD REPLYlink written 18 days ago by cfos4698170
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