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go.R
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rm(list=ls())
options(stringsAsFactors = F)
library(data.table)
library(Seurat)
library(monocle)
library(ROTS)
library(clusterProfiler)
library(ggplot2)
library(clusterProfiler)
library(org.Mm.eg.db)
###########################################
# #
# Load files #
# #
###########################################
de_genes <-read.csv('gene_cluster3.csv')
gene_names <- de_genes$gene
###########################################
# #
# Transfer ID symbol #
# #
###########################################
entrez_genes <- bitr(gene_names, fromType="SYMBOL",
toType="ENTREZID",
OrgDb="org.Mm.eg.db")
entrez_genes <- entrez_genes[!entrez_genes$ENTREZID %in% "101055843",]
#write.csv(entrez_genes, file="entrez_genes.csv")
###########################################
# #
# BP #
# #
###########################################
ego <- enrichGO(gene = entrez_genes$ENTREZID,
OrgDb = org.Mm.eg.db,
ont = "BP",
pAdjustMethod = "BH",
pvalueCutoff = 0.9,
qvalueCutoff = 0.9)
ego=DOSE::setReadable(ego, OrgDb='org.Mm.eg.db',keyType='ENTREZID')
head(ego)
pdf('GO_term_BP_gene_cluster3.pdf',width = 20,height = 10)
dotplot(ego, showCategory=50)
dev.off()
tiff('GO_term_BP_gene_cluster3.tiff',width = 6000,height = 3000, units = "px",res = 300)
dotplot(ego, showCategory=50)
dev.off()
write.csv(ego, file="GO_term_BP_gene_cluster3.csv")
###########################################
# #
# CC #
# #
###########################################
ego <- enrichGO(gene = entrez_genes$ENTREZID,
OrgDb = org.Mm.eg.db,
ont = "CC",
pAdjustMethod = "BH",
pvalueCutoff = 0.9,
qvalueCutoff = 0.9)
ego=DOSE::setReadable(ego, OrgDb='org.Mm.eg.db',keyType='ENTREZID')
head(ego)
pdf('GO_term_CC_gene_cluster3.pdf',width = 11,height = 10)
dotplot(ego, showCategory=50)
dev.off()
tiff('GO_term_CC_gene_cluster3.tiff',width = 3500,height = 3000, units = "px",res = 300)
dotplot(ego, showCategory=50)
dev.off()
write.csv(ego, file="GO_term_CC_gene_cluster3.csv")
###########################################
# #
# MF #
# #
###########################################
ego <- enrichGO(gene = entrez_genes$ENTREZID,
OrgDb = org.Mm.eg.db,
ont = "MF",
pAdjustMethod = "BH",
pvalueCutoff = 0.9,
qvalueCutoff = 0.9)
ego=DOSE::setReadable(ego, OrgDb='org.Mm.eg.db',keyType='ENTREZID')
head(ego)
pdf('GO_term_MF_gene_cluster3.pdf',width = 11,height = 10)
dotplot(ego, showCategory=50)
dev.off()
tiff('GO_term_MF_gene_cluster3.tiff',width = 3500,height = 3000, units = "px",res = 300)
dotplot(ego, showCategory=50)
dev.off()
write.csv(ego, file="GO_term_MF_gene_cluster3.csv")
###########################################
# #
# KEGG #
# #
###########################################
kk <- enrichKEGG(gene = entrez_genes$ENTREZID,
organism = "mmu",
keyType = "kegg",
pAdjustMethod = "BH",
pvalueCutoff = 0.9,
qvalueCutoff =0.9)
kk=DOSE::setReadable(kk, OrgDb='org.Mm.eg.db',keyType='ENTREZID')
head(kk)
pdf('KEGG_gene_cluster3.pdf',width = 11,height = 10)
dotplot(kk, showCategory=50)
dev.off()
tiff('KEGG_gene_cluster3.tiff',width = 3500,height = 3000, units = "px",res = 300)
dotplot(kk, showCategory=50)
dev.off()
write.csv(kk, file="KEGG_gene_cluster3.csv")