I was given a data set that is comparing RNAseq bulk data. It hasthe gene.name and corresponding p value, padj and log2fold change. I was asked to run it through an analysis enrichment pathway, but I am completely lost. I was thinking that I would use with gseKEGG or gseGo. I attatched a sample of the csv file that I have. Does anyone have a simple code that will make this work?
enter image description here Thank you!
I tried to run this:
library(clusterProfiler)
library(org.Mm.eg.db)
data_d3 <- read.csv("I read in the right file")
gene_list <- data_d3$Gene.Name
enrich_result <- enrichKEGG(gene = gene_list, organism = 'mmu', keyType = 'kegg', pvalueCutoff = 0.05
--> No gene can be mapped....
--> Expected input gene ID: 18598,217698,104112,106557,11677,16832
--> return NULL...