function to summary GWAA data

Description

Provides summary of an object of class snp.data-class. Chromosome, map position, allele coding, number of observed genotypes, allelic frequency, genotypic distrbution, P-value of the exact test for HWE, Fmax (estimate of deviation from HWE, allowing meta-analysis) and LRT P-value for HWE test are listed

Usage

	## S3 method for class 'snp.data'
summary(object, ...)

Arguments

Value

Data frame summary for snp.data object

Note

The P-values reported for X-chromosome are based on analysis of female data, but other statistics (frequencies, calls, ...) are based on all data. Statistics for Y-chromosome are based on male-only. P-HWE is not defined for mt- and Y- markers (set to 1.0).

Author(s)

Yurii Aulchenko

References

Wigginton, JE, Cutler, DJ, and Abecasis, GR (2005) A Note on Exact Tests of Hardy-Weinberg Equilibrium. American Journal of Human Genetics. 76: 887-93.

See Also

summary.gwaa.data, snp.data-class

Examples

require(GenABEL.data)
data(srdta)
summary(gtdata(srdta[,1:20]))