library(clusterProfiler)
library(org.Hs.eg.db)
library(tidyverse)
library(DOSE)
library(ReactomePA)
library(enrichplot)
library(fgsea)
library(data.table)
library(ggplot2)
keytypes(org.Hs.eg.db)
res = read.csv("coex.Csv")
head(res)
original_gene_list = res$correlation
names(original_gene_list) <- res$gene
gene_list<-na.omit(original_gene_list)
gene_list = sort(gene_list, decreasing = TRUE)
gse <- gseGO(geneList=gene_list,
ont ="ALL",
keyType = "ENSEMBL",
minGSSize = 3,
maxGSSize = 800,
pvalueCutoff = 0.05,
verbose = TRUE,
scoreType = "pos",
OrgDb = org.Hs.eg.db,
pAdjustMethod = "none")
The result is returned as " preparing geneSet collections... GSEA analysis... leading edge analysis... done... Warning messages: 1: In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (1% of the list). The order of those tied genes will be arbitrary, which may produce unexpected results. 2: In serialize(data, node$con) : 'package:stats' may not be available when loading 3: In serialize(data, node$con) : 'package:stats' may not be available when loading 4: In serialize(data, node$con) : 'package:stats' may not be available when loading 5: In serialize(data, node$con) : 'package:stats' may not be available when loading 6: In serialize(data, node$con) : 'package:stats' may not be available when loading"
why is this happening?
