35 lines
1.1 KiB
R
35 lines
1.1 KiB
R
 
|
suppressMessages(library(dplyr))
|
||
|
|
suppressMessages(library(clusterProfiler))
|
||
|
|
|
||
|
|
Args <- commandArgs(T)
|
||
|
|
setwd("/root/tropical_fruits/tools/kegg/sugarcane")
|
||
|
|
|
||
|
|
|
||
|
|
egg<-read.csv("sugarcane.emapper.annotations",sep="\t",header=T)
|
||
|
|
|
||
|
|
egg[egg==""]<-NA
|
||
|
|
gene2ko <- egg %>%
|
||
|
|
dplyr::select(GID = query, Ko = KEGG_ko) %>%
|
||
|
|
na.omit()
|
||
|
|
|
||
|
|
gene2ko[,2]<-gsub("ko:","",gene2ko[,2])
|
||
|
|
|
||
|
|
load(file = "kegg_info.RData")
|
||
|
|
|
||
|
|
pathway2gene <- gene2ko %>% left_join(ko2pathway, by = "Ko") %>%
|
||
|
|
dplyr::select(pathway=Pathway,gene=GID) %>%
|
||
|
|
na.omit()
|
||
|
|
|
||
|
|
contract_list <- read.csv(paste("sugarcane_", Args[1],".txt",sep = ""),
|
||
|
|
sep="\t",header=T)
|
||
|
|
contract_list <- as.factor(contract_list$gene)
|
||
|
|
|
||
|
|
df<-enricher(gene=contract_list,
|
||
|
|
pvalueCutoff = 0.05,
|
||
|
|
pAdjustMethod = "BH",
|
||
|
|
TERM2GENE = pathway2gene,
|
||
|
|
TERM2NAME = pathway2name)
|
||
|
|
df_final <- as.data.frame(df) %>%
|
||
|
|
select(c("Description","Count","p.adjust","GeneRatio","geneID","BgRatio","ID","pvalue"))
|
||
|
|
write.table(as.data.frame(df_final) ,paste("out_", Args[1],".txt",sep = ""),sep = "\t",quote = F,row.names=T)
|