gibson: Gene expression dataset from Idaghdour et al. (2008)

In jdstorey/edge: Extraction of Differential Gene Expression

Description

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).

Usage

data(gibson)

Format

• 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.

Value

gibson dataset

Note

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/.

References

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.

Examples

# 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)

jdstorey/edge documentation built on May 18, 2019, 11:35 p.m.