nutrimouse {whitening}

Nutrimouse Data

Description

The nutrimouse dataset is a collection of gene expression and lipid measurements collected in a nutrigenomic study in the mouse studying 40 animals by Martin et al. (2007).

Usage

data(nutrimouse)

Format

A list containing the following components:

gene collects gene expression of 120 genes in liver tissue for 40 mice.

lipid collects concentrations of 21 lipids for 40 mice.

diet describes the diet of each mouse ("coc", "fish", "lin", "ref", or "sun").

genotype describes the genotype of each mouse: wild type ("wt") or PPARalpha deficient ("ppar").

Details

This data set is used to illustrate CCA-based data integration in Jendoubi and Strimmer (2019) and is also described in Gonzalez et al. (2008).

Source

The original data are available in the CCA package by Gonzalez et al. (2008), see their function nutrimouse.

References

Gonzalez, I., Dejean, S., Martin, P.G.P, Baccini, A. CCA: an R package to extend canonical correlation analysis. J. Statist. Software 23:1–13 (2008)

Jendoubi, T., Strimmer, K.: A whitening approach to probabilistic canonical correlation analysis for omics data integration. BMC Bioinformatics 20:15 <DOI:10.1186/s12859-018-2572-9>

Martin, P.G.P., Guillou, H., Lasserre, F., Dejean, S., Lan, A., Pascussi, J.-M., Cristobal, M.S., Legrand, P., Besse, P., Pineau, T.: Novel aspects of PPARalpha-mediated regulation of lipid and xenobiotic metabolism revealed through a multigenomic study. Hepatology 54, 767–777 (2007) <DOI:10.1002/hep.21510>

Examples

# load whitening library
library("whitening")

# load nutrimouse data set
data(nutrimouse)

dim(nutrimouse$gene) # 40 120
dim(nutrimouse$lipid) # 40 21
levels( nutrimouse$diet ) #  "coc"  "fish" "lin"  "ref"  "sun"
levels( nutrimouse$genotype ) # "wt"   "ppar"