2020-08-06

R历史纪录
library(clusterProfiler)
library(ggplot2)
library( org.Hs.eg.db)
a <- read.xlsx("c1.xlsx",colNames = F,rowNames = F)
View(a)
go <- enrichGO(a, OrgDb = org.Hs.eg.db, ont='ALL',keyType = 'ENTREZID')
rm(a)
rm(go)
gc()
b <- read.xlsx("c2.xlsx",colNames = F,rowNames = F)
go <- enrichGO(b, OrgDb = org.Hs.eg.db, ont='ALL',keyType = 'ENTREZID')
rm(b)
rm(go)
gc()
c <- read.xlsx("c3.xlsx",colNames = F,rowNames = F)
go <- enrichGO(b, OrgDb = org.Hs.eg.db, ont='ALL',keyType = 'ENTREZID')
go <- enrichGO(c, OrgDb = org.Hs.eg.db, ont='ALL',keyType = 'ENTREZID')
library(DOSE)
go <- enrichGO(c, OrgDb = org.Hs.eg.db, ont='ALL',keyType = 'ENTREZID')
rm(c)
rm(data)
rm(data1)
rm(go)
gc()
a <- read.xlsx("enterzid.xlsx",colNames = T,rowNames = F)
a <- read.xlsx("entrezid.xlsx",colNames = T,rowNames = F)
go <- enrichGO(a, OrgDb = org.Hs.eg.db, ont='ALL',keyType = 'ENTREZID')
View(a)
library(DOSE)
library(GO.db)
library(org.Hs.eg.db)
library(topGO)
library(GSEABase)
library(clusterProfiler)
go <- enrichGO(a, OrgDb = org.Hs.eg.db, ont='ALL',keyType = 'ENTREZID')
library(DOSE)
library(GO.db)
library(org.Hs.eg.db)
library(topGO)
library(GSEABase)
library(clusterProfiler)
go <- enrichGO(a, OrgDb = org.Hs.eg.db, ont='ALL',keyType = 'ENTREZID')
library(org.Hs.eg.db)
library("AnnotationHub")
library("biomaRt")
library("clusterProfiler")
library("topGO")
library("Rgraphviz")
library("pathview")
gogo <- enrichGO(a, OrgDb = org.Hs.eg.db, ont='ALL',keyType = 'ENTREZID')
library(biomaRt)
library(ggplot2)
go1 <- enrichGO(a, OrgDb = org.Hs.eg.db, ont='ALL',keyType = 'ENTREZID')
library(GOplot)
library(ggdendro)
library(GSEABase)
library(topGO)
library(Rcpp)
library(graph)
library(topGO)
library(quantreg)
library(pillar)
library(broom)
library(conquer)
library(GO.db)
library(DO.db)
go2 <- enrichGO(a, OrgDb = org.Hs.eg.db, ont='ALL',keyType = 'ENTREZID')
library(clusterProfiler)
library(ggplot2)
library( org.Hs.eg.db)
class(a)
head(a)
bb <- a$ENTREZID
class(b)
class(bb)
go2go <- enrichGO(bb, OrgDb = org.Hs.eg.db, ont='ALL',keyType = 'ENTREZID')
dotplot(go2go)
rm(a)
rm(go2go)
rm(bb)
rm(go)
rm(go1)
rm(go2)
rm(gogo)
gc()
library(clusterProfiler)
library(ggplot2)
library( org.Hs.eg.db)
library(openxlsx)
a <- read.xlsx("c1.xlsx",colNames = F,rowNames = F)
class(a)
View(a)
a1 <- a$X1
goa1 <- enrichGO(a1, OrgDb = org.Hs.eg.db, ont='ALL',keyType = 'ENTREZID')
View(goa1)
goa1@gene
dotplot(goa1)
barplot(ggoa1)
barplot(goa1)
dim(go)
dim(goa1)
heatplot(goa1)
View(geneSets)
View(goa1$geneSets)
goa1@geneSets
View(goa1@geneSets)
ego <- enrichGO(a1, OrgDb = org.Hs.eg.db, ont = "ALL",pvalueCutoff = 0.05,qvalueCutoff = 0.05, readable = TRUE,keyType = "ENTREZID")
View(goa1@result)
write.csv(goa1@result,"goa1result.csv")
rm(a)
rm(ego)
rm(goa1)
rm(a1)
gc()
library("openxlsx")
library("clusterprofiler")
library("clusterProfiler")
a <- read.xlsx("c1.xlsx")
class(a)
b <- as.list(a)
class(b)
mode(a)
mode(b)
c <- 3
mode(c)
go <- enrichGO(b, OrgDb=org.Hs.eg.db, keyType = "ENTREZID", ont = "BP",pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2, minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
library("org.Hs.eg.db")
go <- enrichGO(b, OrgDb=org.Hs.eg.db, keyType = "ENTREZID", ont = "BP",pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2, minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
go <- enrichGO(b, OrgDb=org.Hs.eg.db, keyType = "ENTREZID", ont = "ALL",pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2, minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
FO <- enrichGO(b, OrgDb=org.Hs.eg.db, keyType = "ENTREZID", ont = "ALL",pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2, minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
View(b)
View(a)
View(b)
View(b)
rm(a)
rm(b)
rm(c)
rm(FO)
rm(GO)
rm(go)
ls
ls()
ls
gc()
a <- read.xlsx("c1.xlsx",rowNames = F,colNames = F)
b <- as.list(a)
rm(b)
gc()
b <- a[,1]
class(b)
View(b)
go <- enrichGO(b, OrgDb=org.Hs.eg.db, keyType = "ENTREZID", ont = "BP",pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2, minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
barplot(go)
View(go)
gogo <- enrichGO(b, OrgDb=org.Hs.eg.db, keyType = "ENTREZID", ont = "BP",minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
write.csv(go,file = "result.csv")
rm(go)
rm(gogo)
gc()
go1 <- enrichGO(b, OrgDb=org.Hs.eg.db, keyType = "ENTREZID", ont = "ALL",minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
write.csv(go1,file = "result1.csv")
write.csv(go1,file = "result1.csv")
rm(a)
rm(b)
gc()
a <- read.xlsx("c2.xlsx",colNames = F,rowNames = F)
b <- a$X1
View(a)
go2 <- enrichGO(b, OrgDb=org.Hs.eg.db, keyType = "ENTREZID", ont = "ALL",minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
write.csv(go2,file = "result2.csv")
rm(a)
rm(b)
gc()
a <- read.xlsx("c3.xlsx",colNames = F,rowNames = F)
b <- a$X1
go3 <- enrichGO(b, OrgDb=org.Hs.eg.db, keyType = "ENTREZID", ont = "ALL",minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
write.csv(go3,file = "result3.csv")
rm(a)
rm(b)
a <- read.xlsx("c4.xlsx",colNames = F,rowNames = F)
b <- a$X1
go4 <- enrichGO(b, OrgDb=org.Hs.eg.db, keyType = "ENTREZID", ont = "ALL",minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
write.csv(go4,file = "result4.csv")
rm(a)
rm(b)
a <- read.xlsx("c5.xlsx",colNames = F,rowNames = F)
b <- a$X1
go5 <- enrichGO(b, OrgDb=org.Hs.eg.db, keyType = "ENTREZID", ont = "ALL",minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
write.csv(go5,file = "result5.csv")
rm(a)
rm(b)
gc()
a <- read.xlsx("c6.xlsx",colNames = F,rowNames = F)
b <- a$X1
go6 <- enrichGO(b, OrgDb=org.Hs.eg.db, keyType = "ENTREZID", ont = "ALL",minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
write.csv(go6,file = "result6.csv")
a <- read.csv(result1.csv)
a <- read.csv("result1.csv")
rm(a)
rm(go1)
rm(go2)
rm(go3)
rm(go4)
rm(go5)
rm(go6)
rm(b)
gc()
a <- read.xlsx("zong.xlsx",colNames = F,rowNames = F)
b <- a$X1
go <- enrichGO(b, OrgDb=org.Hs.eg.db, keyType = "ENTREZID", ont = "ALL",minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
write.csv(go,file = "go.csv")
go <- enrichKEGG(b, OrgDb=org.Hs.eg.db, keyType = "ENTREZID")
go <- enrichKEGG(b, keyType = "ENTREZID")
go <- enrichKEGG(b, keyType = "kegg")
dotplot(go)
rm(a)
rm(go)
rm(b)
gc()