R: Permutation test analysis

permTest {SNPassoc} | R Documentation

## Permutation test analysis

### Description

This function extract the p values for permutation approach performed using scanWGassociation function

### Usage

       permTest(x, method="minimum", K)

### Arguments

`x` | a required object of class 'WGassociation' with the attribute 'permTest'. See details
`method` | statistic used in the permutation test. The default is 'minimum' but 'rtp' (rank truncated product) is also available.
`K` | number of the K most significant p values from the total number of test performed (e.g number of SNPs) used to compute the rank truncated product. This argument is only required when method='rtp'. See references

### Details

This function extract the p values from an object of class 'WGassociation'. This object migth be obtained using the funcion called 'scanWGassociation' indicating the number of permutations in the argument 'nperm'.

### Value

An object of class 'permTest'.

'print' returns a summary indicating the number of SNPs analyzed, the number of valid SNPs (those non-Monomorphic and that pass the calling rate), the p value after Bonferroni correction, and the p values based on permutation approach. One of them is based on considering the empirical percentil for the minimum p values, and the another one on assuming that the minimum p values follow a beta distribution.

'plot' produces a plot of the empirical distribution for the minimum p values (histogram) and the expected distribution assuming a beta distribution. The corrected p value is also showed in the plot.

See examples for further illustration about all previous issues.

### References

Dudbridge F, Gusnanto A and Koeleman BPC. Detecting multiple associations in genome-wide studies. Human Genomics, 2006;2:310-317.

Dudbridge F and Koeleman BPC. Efficient computation of significance levels for multiple associations in large studies of correlated data, including genomewide association studies. Am J Hum Genet, 2004;75:424-435.

JR Gonzalez, L Armengol, X Sole, E Guino, JM Mercader, X Estivill, V Moreno. SNPassoc: an R package to perform whole genome association studies. Bioinformatics, 2007;23(5):654-5.

### See Also

`scanWGassociation`

### Examples

    data(SNPs)
    datSNP<-setupSNP(SNPs,6:40,sep="")
    ans<-scanWGassociation(casco~1,data=datSNP,model="co",nperm=1000)

    # pPerm<-permTest(ans)
    # print(pPerm)
    # plot(pPerm)

[Package SNPassoc version 1.9-2 Index]