### This an example to run kMEn.R on a single patient.

# load in the kMEn function
source('./kMEn.R')
# load in gene set annotations
load('./GO_list.RData',verbose = T)
# load in the example dataset
dat <- read.csv('./exampleData_kMEn.csv',row.names=1)

# run kMEn
res_singlePatient <- kMEn(f.absLogFC(dat[,1],dat[,2]), gene.symbol = rownames(dat), GeneSet.list = GO_list, FDR.method = 'BY')

# Pathway level result
head(res_singlePatient$Pathway)
# Gene level result
head(res_singlePatient$DEG)