Commit 193afe13 authored by Patino Medina, Laura's avatar Patino Medina, Laura
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.libPaths(c('/local/data/course/project/araformatics/pipeline/test_R',.libPaths()))
#!/usr/bin/env Rscript
#BIF30806 Project group: Araformatic
#(2021)
#KEGG pathway enrichment
#Scrip to run enrichKEGG, from clusterProfile library to get enriched
#KEGG pathways and their adjusted p values.
#Usage: Rscript KEGG3.R input_file.txt
# input_file: txt file, genes as rows, leafs as columns and values
# are adjusted p value from DGE
#Output: txt file for each leaf(sample) in the input file
#source("https://bioconductor.org/biocLite.R")
#biocLite(c("KEGGREST", "org.At.tair.db", "Rgraphviz","clusterProfile"))
#if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
#BiocManager::install("org.At.tair.db")
#BiocManager::install("signatureSearch")
#BiocManager::install("clusterProfiler")
library("org.At.tair.db")
library(KEGGREST)
library(clusterProfiler)
#Take arguments from command line
args = commandArgs(trailingOnly = TRUE)
#Get A.thaliana pathways from KEGG
pathway_list <- keggList("pathway", "ath")
#genes per pathway
pathway_codes <- sub("path:", "", names(pathway_list)) #remove path: string
genes_pathway <- sapply(pathway_codes,
function(pwid){
path <- keggGet(pwid)
if (is.null(path[[1]]$GENE)) return(NA)
path2 <- path[[1]]$GENE[c(TRUE,FALSE)]
path2 <- unlist(lapply(strsplit(path2,split=";",fixed =T),
function(x)x[1])) #atomic vector, apply function to all [1] in path2
return(path2)
})
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(args[1],stringsAsFactors = F,row.names = 1)
sample_names <-colnames(de_multiple)
for(leaf in sample_names){
current_leaf = leaf
print(current_leaf)
#geneList
geneList <- rownames(de_multiple[which(de_multiple[which(colnames(de_multiple) == current_leaf)]<0.05),])
print(geneList)
#enrichment
kk <- enrichKEGG(gene=geneList,organism="ath",keyType = "kegg",
pAdjustMethod= "BY",universe=names(all_geneIDs),qvalueCutoff = 0.05)
#write table with enriched pathways
if(is.null(kk)){
next
}
else{
#enrichKEGG2 gives a A feaResult instance turn it into data frame
enrich_k = data.frame(kk@result)
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)
}
}
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