tMatFunction: computing t statistics for each phentoype at each marker

In reGenotyper: Detecting Mislabeled Samples in Genetic Data

Description

A subfunction used by main function to compute the t statistic for each phenotype at each marker.

Usage

tMatFunction(mytrait, mygt, fileName = "")

Arguments

mytrait	phenotype data: a nTrait-by-nSample matrix
mygt	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.
fileName	name for temporary output file during computing process. Default=NULL

Value

a matrix with nTrait x nMarker with t.statistics

Note

To improve the efficiency of computing, the technique of matrixeQTL (by Andrey A. Shabalin) has been used.

Author(s)

Yang Li <[e-mail]>

References

Li Y. et al, reGenotyper: detecting mislabeled samples in genetic data (submitted).
Shabalin A. A., Matrix eQTL: ultra fast eQTL analysis via large matrix operations, Bioinformatics (2012) 28 (10): 1353-1358.

See Also

reGenotyper

Examples

  data(phenotype)
  data(genotype)
  t.mat <- tMatFunction(phenotype, genotype, fileName = "test")

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