mice: Heterogenous stock mice population

In synbreedData: Data for the Synbreed Package

Description

Data set comprises public available data of 2527 (1293 males and 1234 females) heterogenous stock mice derived from eight inbred strains (A/J, AKR/J, BALBc/J, CBA/J, C3H/HeJ, C57BL/6J, DBA/2J and LP/J) followed by 50 generations of pseudorandom mating. All individuals are labeled with a unique ID, starting with A048005080. For all individuals, family, sex (females=0, males=1), month of birth (1-12), birthyear, coat color, cage density and litter is available and stored in covar.

The measured traits are described in Solberg et al. (2006). Here, the body weight at age of 6 weeks [g] and growth slope between 6 and 10 weeks age [g/day] are available. The heritabilities of these traits are reported as 0.74 and 0.30, respectively (Valdar et al, 2006b). Phenotypic data was taken from http://mus.well.ox.ac.uk/GSCAN/HS_PHENOTYPES/Weight.txt.

Genotypic data consists of 12545 biallelic SNP markers and is available for 1940 individuals. Raw genotypic data from http://mus.well.ox.ac.uk/GSCAN/HS_GENOTYPES/ is given in the Ped-File Format with two columns for each marker. Both alleles were combined to a single genotype for each marker in mice data. The SNPs are mapped in a sex-averaged genetic map with distances given in centimorgan (Shifman et al. (2006)). SNPs are mapped across all 19 autosomes and X-chromosome where distances between adjacent markers vary form 0 to 3 cM.

Usage

data(mice)

Format

Object of class gpData

Source

Welcome Trust Centre for Human Genetics, Oxford University, data available from http://gscan.well.ox.ac.uk

References

Shifman S, Bell JT, Copley RR, Taylor MS, Williams RW, et al. (2006) A High-Resolution Single Nucleotide Polymorphism Genetic Map of the Mouse Genome. PLoS Biol 4(12)

Solberg L.C. et al. (2006), A protocol for high-throughput phenotyping, suitable for quantitative trait analysis in mice. Mamm. Genome 17, 129-146

Valdar W, Solberg LC, Gauguier D, Burnett S, Klenerman P, Cookson WO, Taylor MS, Rawlins JN, Mott R, Flint J. (2006a) Genome-wide genetic association of complex traits in heterogeneous stock mice. Nat Genet. 8, 879-887.

Valdar W, Solberg LC, Gauguier D, Cookson WO, Rawlins NJ, Mott R, Flint J.(2006b) Genetic and environmental effects on complex traits in mice. Genetics 175, 959-984

Examples

## Not run: 
library(synbreed)
data(mice)
summary(mice)

## End(Not run)

synbreedData documentation built on May 1, 2019, 6:51 p.m.