work/epsd-hyperTest.R

In twesleyb/Uezu2016: iBioID Proteomics from Uezu, Kanak, Bradshaw et al., 2016

#!/usr/bin/ Rscript

# this code chunk is associate with dlg4 network

root = getrd()

library(dplyr)
library(data.table)

#library(Uezu2016)
devtools::load_all()
data(epsd)
data(epsd_bioid)

library(geneLists)

# see all available gene lists
geneLists()

# load the SFARI genes
data("sfariGene",package="geneLists")
data("sfariAnimal",package="geneLists")

# use all genes identified in proteomics experiment as background
all_entrez <- unique(epsd_bioid$Entrez)

# combine SFARI gene lists 
sfari <- c(sfariGene[["ASD"]], sfariAnimal[["ASD"]])

# test for enrichment of sfari genes in DLG4 proteome
geneLists::hyperTest(sfari,epsd,background=all_entrez)

geneLists::getIDs(epsd[epsd %in% sfari], "entrez", "symbol", "mouse")