R: function to summary GWAA data

summary.snp.data {GenABEL} | R Documentation

## 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

`object` | snp.data object
`...` | additional arguments (not used)

### 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]))

[Package GenABEL version 1.8-0 Index]