Commit 27828b4f authored by Patino Medina, Laura's avatar Patino Medina, Laura
Browse files

Replace KEGG1_enrichment.R

parent 193afe13
......@@ -13,7 +13,7 @@
#source("https://bioconductor.org/biocLite.R")
#biocLite(c("KEGGREST", "org.At.tair.db", "Rgraphviz","clusterProfile"))
#if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# install.packages("BiocManager")
#BiocManager::install("org.At.tair.db")
#BiocManager::install("signatureSearch")
#BiocManager::install("clusterProfiler")
......@@ -45,7 +45,7 @@ all_geneIDs <- keys(org.At.tair.db)
#Read DE file
#MULTIPLE SAMPLES IN ONE FILE
#read file with p adj value data
de_multiple<- read.delim("multiple_input.txt",stringsAsFactors = F,row.names = 1)
#de_multiple<- read.delim("multiple_input.txt",stringsAsFactors = F,row.names = 1)
de_multiple<- read.delim(args[1],stringsAsFactors = F,row.names = 1)
sample_names <-colnames(de_multiple)
......@@ -72,7 +72,7 @@ for(leaf in sample_names){
table = paste(current_leaf,"KEGG1",sep="_")
table = paste(table,"txt",sep=".")
write.table(enrich_k, col.names=T, row.names=F,
file = paste("/enrichment/",table,sep=""), sep ="\t",quote = F)
file = paste("enrichment/",table,sep=""), sep ="\t",quote = F)
}
......
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