cp_enrichment
Scripts for enrichment of KEGG pathways using clusterProfiler
Enrichment analysis of KEGG pathways using clusterProfiler packge in R
This repository shows how to perform enrichment analysis of KEGG pathways in non-model organisms using the clusterProfiler in R. Please visit https://yulab-smu.top/biomedical-knowledge-mining-book/ for any doubt or detailed instructions to set up parameters of your enrichment analysis or visualize your results in fancy plots.
Programs and files required before initiating with this tutorial:
-R and RStudio installed in your computer
-
clusterProfiler package installed in R
-
To generate an input file from genome functional annotation outputs with eggnog. This input file must tab-separated and header (column names), see example:
Example of input file 1:
| ID | KEGG (ko:Knumber) |
|---|---|
| Tatro_000080-T1 | ko:K14779 |
| Tatro_000081-T1 | ko:K04567 |
| Tatro_000082-T1 | ko:K11340,ko:K11400,ko:K11652 |
| Tatro_000083-T1 | - |
-List of IDs to be analyzed like input file 2 in .txt
Example 1 of input file 2:
| ID |
|---|
| Tatro_005212-T1 |
| Tatro_000081-T1 |
| Tatro_002393-T1 |
| Tatro_003445-T1 |
| … |
Example 2 of input file 2:
| ID | logFC | logCPM | F | PValue | FDR |
|---|---|---|---|---|---|
| Tatro_002208-T1 | -1.843 | 5.400 | 97.038 | 1.756e-09 | 5.520e-06 |
| Tatro_011096-T1 | -1.203 | 5.524 | 95.278 | 2.069e-09 | 5.520e-06 |
| Tatro_008592-T1 | -1.540 | 6.419 | 93.472 | 2.455e-09 | 5.520e-06 |
Perform KEGG pathway enrichment analysis in R
Here you can see the R script for the enrichment analysis using clusterprofiler.