clusterProfiler gene list retrieval
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Entering edit mode
19 months ago
LacquerHed ▴ 20

I am interested in retrieving genes that fell into a specific gene category with clusterProfiler as follows:

Subcluster2n3_KO_DOWN_gene_symbols <- readLines("Subcluster2n3_KO_DOWN.txt")

Subcluster2n3_KO_DOWN_geneList <- mapIds(org.Mm.eg.db,Subcluster2n3_KO_DOWN_gene_symbols,'ENTREZID','SYMBOL')

Subcluster2n3_KO_DOWN_KEGG <- enrichKEGG(Subcluster2n3_KO_DOWN_geneList,organism="mmu",pvalueCutoff=0.05, qvalueCutoff=0.05, pAdjustMethod="fdr")

> Subcluster2n3_KO_DOWN_KEGG$Description
 [1] "Protein digestion and absorption"                         
 [2] "Peroxisome"                                               
 [3] "Bile secretion"                                           
 [4] "Proximal tubule bicarbonate reclamation"                  
 [5] "Mineral absorption"

I just want to know which genes from my list were mapped under each category, not sure how to retrieve that info. Thanks.

clusterProfiler GO KEGG Reactome ontology • 672 views
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Entering edit mode
10 months ago
Guangchuang Yu ★ 2.5k

see the FAQ.

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