Functional enrichment analysis of bacteria
I have gene lists from an RNA-seq experiment from E.coli bacteria. So far, I have only worked with model organisms, which are supported by biomaRt, so conversion of gene IDs and functional enrichment analysis within R was easy. Now that I am working with a bacterial dataset for which there is no biomaRt support, I am a bit uncertain. After searching around, I decided to use the DAVID web interface. From there, I exported the results from the functional annotation clustering as .txt files (using all 3 GO term databases, i.e. BP, CC and MF). These have the following structure:
Annotation Cluster 1 Enrichment Score: 2.0813446807310627 Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR GOTERM_CC_DIRECT ... Annotation Cluster 2 Enrichment Score: 0.028318244118032198 Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR GOTERM_BP_DIRECT ...
I would like to visualize these results within R. Is there a function for example using the clusterProfiler package that I am not aware of?
Or is this maybe not the best approach and there is a more suitable one?
I would really appreciate some help!
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