get.sig.thr {DOQTL} | R Documentation

## Get the significance thresholds.

### Description

Given a set of permutations, return the significance thresholds on the autosomes and X chromosome.

### Usage

      get.sig.thr(perms, alpha = 0.05, Xchr = TRUE)

### Arguments

`perms` | Numeric matrix with the maximum LOD (or maximum -log10(p-value)) from each permuation.
`alpha` | Numeric vector containing the alpha level of the significance thresholds.
`Xchr` | Logical value (default = TRUE) that indicates that the permutations contain both autosomal and X chromosome thresholds.

### Value

Numeric matrix containing the significance thresholds for the autosomes in column 1 an dthe X chromossome in column 2.

### Author(s)

Daniel Gatti

### 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.pgw`

### 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]