gibson {edge} | R Documentation |
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 (AGADIR).
data(gibson)
batch: Batches in experiment.
location: Environment/lifestyle of Moroccan Amazigh groups.
gender: Sex of individuals.
gibexpr: A 500 rows by 46 columns matrix of gene expression values.
gibson dataset
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 http://genomine.org/de/.
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.
# import data(gibson) 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 summary(de_odp)