Gene Enrichment

Question

[iamsmor]

Hi Everyone ı am trying to do enrichment. In my recent post ı meantionedGene enrichment analysis R studio error about first error that ı accrossed. I tide over it by import gmt file rstudio manually.

library(readr)
c7_all_v7_1_entrez <- read_table2("~/workspace1/rnaseq/gene_enrichment/c7.all.v7.1.entrez.gmt", 
    col_names = FALSE)
library(readr)
c6_all_v7_1_entrez <- read_table2("~/workspace1/rnaseq/gene_enrichment/c7.all.v7.1.entrez.gmt", 
    col_names = FALSE)

But ı got errors in following steps so ı amnot sure ı completely overcome first error or It causes to error in following steps.So ı need recomment.

myEntrezIdList<- c(4744, 5816, 27286, 94121, 4741, 441631, 3736,9173, 22987, 4142, 6279, 127833, 2840, 56999, 91683, 5122, 2828, 9021, 100192386, 2316, 6134)

ImmunSigEnrich <- enricher(myEntrezIdList,TERM2GENE=c6, pvalueCutoff = 0.01) Error in path2gene[[2]] : subscript out of bounds

ImmunSigEnrich <- setReadable(ImmunSigEnrich, OrgDb = org.Hs.eg.db, keyType = "ENTREZID") Error in is(x, "enrichResult") : object 'ImmunSigEnrich' not found

thank you

[Shred]

Fix typos in your question and be more specific, in the title yet in the question itself.

Answer 1

[Shred]

There's no need to import two times the same library. Do not overpost: rather ask a more detailed question. Read your gmt file using read.gmt() function of clusterProfiler and pass the element to the TERM2GENE parameter in enricher function. Read the clusterProfiler documentation for more.