Commit 7d689b4f authored by Patino Medina, Laura's avatar Patino Medina, Laura
Browse files

Replace GOenrichment_proj.R

parent 1feb0c33
.libPaths(c('/local/data/course/project/araformatics/pipeline/test_R',.libPaths()))
#!/usr/bin/env Rscript
#BIF30806 Project group: Araformatic
#(2021)
#GO enrichment
......@@ -7,11 +7,11 @@
#expression analysis
# Scrip written based on:
# https://ucdavis-bioinformatics-training.github.io/2018-June-RNA-Seq-Workshop/friday/enrichment.html
# Documentation available of topGO usage
# https://www.r-bloggers.com/2015/09/passing-arguments-to-an-r-script-from-command-lines/
# Documentation available on topGO usage
#Usage: Rscript GOenrichment_proj.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 and a pdf GO graph for each leaf(sample) in the input file
#Take arguments from command line
args = commandArgs(trailingOnly = TRUE)
......@@ -26,10 +26,10 @@ if (length(args)==0) {
#Install packages from source.
source("https://bioconductor.org/biocLite.R")
biocLite(c("topGO", "KEGGREST", "org.At.tair.db", "Rgraphviz"))
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
#source("https://bioconductor.org/biocLite.R")
#biocLite(c("topGO", "KEGGREST", "org.At.tair.db", "Rgraphviz"))
#if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
#BiocManager::install("topGO")
#BiocManager::install("AnnotationDbi")
......@@ -44,9 +44,8 @@ library(Rgraphviz)
library(multtest, verbose = FALSE)
####### ADJUSTED P-VALUE #http://rileylab.org/wp-content/uploads/2016/08/multtest.pdf
#useful info: #multiple_dexp[,c(1,which(colnames(multiple_dexp) == current_leaf))]
#GO enrichment on multiple leafs(samples)
#GO enrichment on multiple leaves(samples)
#list with samples names
multiple_dexp<- read.delim(args[1],stringsAsFactors = F)
......@@ -74,7 +73,7 @@ for(leaf in sample_names[2:length(sample_names)]){
geneSelectionFun = function(x)(x == 1),
annot = annFUN.org, mapping = "org.At.tair.db")
#Run the Fishers exact Test (raw p-vals)
#Run the Fishers exact Test (raw p-vals)
fisher_sample <- runTest(GOdata_sample, algorithm = "elim", statistic = "fisher")
sample_result <- GenTable(GOdata_sample, raw.p.value = fisher_sample,
......
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