gibson {edge} | R Documentation

## Gene expression dataset from Idaghdour et al. (2008)

### 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)

[Package edge version 2.12.2 Index]