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