rowHWEs: Rowwise Test for Hardy-Weinberg Equilibrium
In scrime: Analysis of High-Dimensional Categorical Data Such as SNP Data

Description Usage Arguments Value Author(s)

Tests for each row of a matrix whether the Hardy-Weinberg Equilibrium holds for the SNP represented by the row.

1	rowHWEs(x, levels = 1:3, affy = FALSE, check = TRUE)

`x`	a matrix in which each row represents a SNP and each column a subject, where the SNPs can take the values specified by `levels`. NAs are allowed.
`levels`	a vector of length three specifying the values with which the three genotypes of each SNP are represented. It is assumed that the second element of `levels` represents the heterozygous genotype, whereas the first and the third element represent the homozygous genotypes. Ignored if `affy = TRUE`.
`affy`	logical specifying whether the SNPs in `x` are coded as in the Affymetrix standard output. If `TRUE`, `levels = c("AA", "AB", "BB")` will be used.
`check`	should some checks be done if, e.g., other than the specified `levels` are used in `x`? It is highly recommended to leave `check = TRUE`. Setting `check = FALSE` will reduce the computation time slightly.

A list containing the values of the ChiSquare statistic for testing for deviation from HWE (stats) and the raw p-values (rawp) computed by employing the ChiSquare distribution with 1 degree of freedom.

Holger Schwender, holger.schwender@udo.edu

scrime documentation built on May 2, 2019, 10:24 a.m.