permutation: performing permutation for estimating the likelihood of a real sample being mislabeled.

Description

a function to performing permutation for getting the distribution of score for a sample with permuted genotype. The resutled distribution will be used to obtain the likelihood of a real sample being mislabeled.

Usage

permutation(pheno, gt, n.permu, process = TRUE, fileName = "", t.thres = 1.5)

Arguments

pheno

phenotype data: a nTrait-by-nSample matrix

genotype data: a nMarker-by-nSample matrix with two allels being 0 and 1 (or A and B) or three allels being 0, 0.5 and 1 (or, A, H, and B), where 0.5 (or H) represents heterozygous allele.

n.permu

The number of permutation to be performed. n.permu=1000 is usually recommended for a reliable estimate but it can take long time.

process

If TRUE, it prints which step has been finished. Default = TRUE.

fileName

name for temporary output file during computing process. Default=NULL

t.thres

threshold for deciding significant QTLs (t.test) that will be used to detecting mislabled samples

Value

a vector with the length of n.permu. Each element represents the score of a randomly selected sample with permutated genotype, only when permu=TRUE.

Details

This function can be used either directly or by the main function reGenotyper.

References

Li Y. et al, reGenotyper: detecting mislabeled samples in genetic data (submitted)

Examples

Run this code

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

Run the code above in your browser using DataLab