Ah yes I forgot to mention your new tool. Thanks for putting it.
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Enrichment analysis specifically by topGO
Hello all,
I am having data frame in R with name of genes in one column and GO description in second column .
Is it possible to know how to get p-value as part of enrichment for each genes in third column .
So through TopGO I am getting different errors.
1 RALBP1 ATPase activity, coupled to movement of substances 2 RALBP1 Rac GTPase binding 3 RALBP1 Ral GTPase binding
Thanks a lot
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2 answers
You can use clusterProfiler.
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Why don't you try this tools which exactly does the same, Gene Set Clustering based on Functional annotation (GeneSCF)
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Take a look at this thread as to how to work programmtically in R
Have your tried to check the manual? You have to download the required db and then parse your list of genes as a vector and select the GO category and output the GO terms. The enrichment is Fisher test. Take a look at the manual from page 3
This R code is for Human micro-array data using
topGOThere is also GOstats package which has the R code in this link that can do the enrichment and generate reports. Take a look
If you want GO enrichment pvalues you can use
DAVID/EnrichR/GOrilla/Panther. They will give the number of genes enriched with also pvalue from the fisher test score. Just supply your gene list and put your desired species or even a background set of genes and perform GO enrichment.There are many ways to perform this.