Commit f4ca7176 authored by Patino Medina, Laura's avatar Patino Medina, Laura
Browse files

Update GOenrichment_proj.R

parent 2dbcd896
......@@ -31,11 +31,11 @@ biocLite(c("topGO", "KEGGREST", "org.At.tair.db", "Rgraphviz"))
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("topGO")
BiocManager::install("AnnotationDbi")
BiocManager::install("org.At.tair.db")
BiocManager::install("Rgraphviz")
BiocManager::install("multtest")
#BiocManager::install("topGO")
#BiocManager::install("AnnotationDbi")
#BiocManager::install("org.At.tair.db")
#BiocManager::install("Rgraphviz")
#BiocManager::install("multtest")
library(topGO)
library("org.At.tair.db")
library(KEGGREST)
......@@ -74,7 +74,7 @@ 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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