get.pgw {DOQTL} | R Documentation

## Get the genome wide p-value.

### Description

Given a set of permutations and a LOD or -log10(p-value), return the adjusted genome-wide p-value. This requires autosomal and X chromosome permutation values as provided by `scanone.perm`. If you are using p-values, make sure to convert both the permutations and the p-values to -log10(-p-value).

### Usage

      get.pgw(stat, chr, perms)

### Arguments

`stat` | Numeric vector of mapping statistics. Must be either LOD or -log10(p-values).
`chr` | Numeric vector of same legnth as stat containing the chromosome on which each statistic occurs.
`perms` | Numeric matrix with the maximum LOD (or maximum -log10(p-value)) from each permuation.

### Value

Numeric vector containing the adjusted genome-wide p-value for each statistic.

### Author(s)

Daniel Gatti, Petr Simecek

### References

The X chromosome in quantitative trait locus mapping. Broman KW, Sen S, Owens SE, Manichaikul A, Southard-Smith EM, Churchill GA. Genetics. 2006 Dec;174(4):2151-8.

### See Also

`get.sig.thr`

### Examples

      ## Not run:
        perms = scanone.perm(pheno = pheno, probs = probs, addcovar = addcovar, snps = anps)
        get.sig.thr(perms)

    ## End(Not run)

[Package DOQTL version 1.19.0 Index]