enrichKEGG results for non-model organism
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AP • 0
@ap-14194
Last seen 8 months ago
United States

Hey everyone,

In order to do gene enrichment analysis on non-model organism (fungi), I obtained the KEGG ids using KOfam analysis. Using clusterProfiler enrichKEGG function I did the enrichment analysis. But the problem now is the enriched pathways I am getting is human diseases like Parkinsons disease, Huntington diseases etc. or human related pathways. Is there a way to filter these out or I am doing something wrong. My codes are given below:


file <- read.delim("T161_core.txt", header = FALSE, sep="\t")
colnames(file) <- c("ProteinID", "KO")
file1<- (file$KO)

kegg <- enrichKEGG(  file1,  organism = "ko",  keyType = "kegg",  pvalueCutoff = 0.05,
                     pAdjustMethod = "BH", qvalueCutoff = 0.05)

p<- dotplot(kegg, showCategory=20) + ggtitle("T161 Core ")
p + theme(
  plot.title = element_text(color="black", size=14, face="bold", hjust=0.5))



sessionInfo( )

Top 20 pathways

clusterProfiler enrichment KEGG • 498 views
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can you tell me the formate of output file from KOfam please? I don't understand the formate of input file for ClusterProfiler.

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