% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/edge.R
\title{Gene expression dataset from Idaghdour et al. (2008)}
  \item batch: Batches in experiment.
  \item location: Environment/lifestyle of Moroccan Amazigh groups.
  \item gender: Sex of individuals.
  \item gibexpr: A 500 rows by 46 columns matrix of gene expression values.
gibson dataset
The data provide gene expression measurements in peripheral blood leukocyte
samples from three Moroccan groups leading distinct ways of life:
desert nomadic (DESERT), mountain agrarian (VILLAGE), and coastal urban
These data are a random subset of 500 genes from the total number of genes
in the original data set. To download the full data set, go to
# import
batch <- gibson$batch
gender <- gibson$gender
location <- gibson$location
gibexpr <- gibson$gibexpr
cov <- data.frame(Batch = batch, Gender = gender,
Location = location)

# create deSet for experiment- static experiment
mNull <- ~Gender + Batch
mFull <- ~Gender + Batch + Location

# create deSet object
de_obj <- build_models(gibexpr, cov = cov, full.model = mFull,
null.model = mNull)

# Perform ODP/lrt statistic to determine significant genes in study
de_odp <- odp(de_obj, bs.its = 10)
de_lrt <- lrt(de_obj, nullDistn = "bootstrap", bs.its = 10)

# summarize significance results
Idaghdour Y, Storey JD, Jadallah S, and Gibson G. (2008) A genome-wide gene
expression signature of lifestyle in peripheral blood of Moroccan Amazighs.
PLoS Genetics, 4: e1000052.