permutation: performing permutation for estimating the likelihood of a...

In reGenotyper: Detecting Mislabeled Samples in Genetic Data

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
gt	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

Details

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

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.

Author(s)

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

References

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

See Also

reGenotyper

Examples

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

Example output

Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: MatrixEQTL

reGenotyper documentation built on May 1, 2019, 11:08 p.m.