ASPBay (version 1.2)

ASP.Selection: Select a subset of SNPs

Description

Select a subset of SNPs using discrimination method for affected sib pairs

Usage

ASP.Selection(Tem_Gen, Index_Gen, IBD, k = log(10000))

Arguments

Tem_Gen

Genotypes of controls (denoted by the number of alternative allele)

Index_Gen

Genotypes of index cases

IBD

IBD states for each affected sib pair

k

Selection threshold (by default log(1e4))

Value

score

The values of the score statistic for each SNPs

stat

The values of discrimination statistic comparing each SNPs with the most associated SNP

SNP_subset

The indexes (numbers of columns) of selected SNPs

SNPname_subset

The names (names of columns) of selected SNPs

Details

Take the genotypes of controls and index cases and the IBD states. Give the score statistics, discrimination statistics and the subset of selected SNPs with the chosen threshold.

References

Dandine-Roulland, Claire and Perdry, Herve. Where is the causal variant? On the advantage of the family design over the case-control design in genetic association studies. Submitted to Eur J Hum Genet

See Also

ASP.Score, ASP.Bayesian

Examples

data(ASPData)
ASP.Selection(ASPData$Control, ASPData$Index, ASPData$IBD )