geno.freq: Summarizing Genotypic Data

In nyiuab/BhGLM: Bayesian hierarchical GLMs and survival models, with applications to Genomics and Epidemiology

Description

This function is to calculate frequecies of missing data, three genotypes, and MAF (minor allelic frequecies), and to test Hardy-Weinberg Equilibrium (HWE) for each marker.

Usage

geno.freq(geno, freq = TRUE, digits = 4, verbose = FALSE) 

Arguments

geno	a matrix of genotypic data.
freq	logical. Shows frequencies or counts.
digits	digits to round with print.
verbose	logical. If TRUE, print out markers removed or with only two genotypes.

Value

This function returns a matrix consisting of frequecies of missing data, three genotypes, MAF (minor allelic frequecies), and p-value for testing HWE.

Author(s)

Nengjun Yi, [e-mail]

Examples

library(BhGLM)

x = sim.x(n=100, m=10, genotype=6:10)
geno = x[, 6:10] #get genotype data
geno.freq(geno, freq=TRUE)
geno.freq(geno, freq=FALSE)

nyiuab/BhGLM documentation built on Jan. 9, 2022, 3:31 p.m.