makeZ: Make a centered (scaled) genetic marker matrix

In digiYozhik/msc_thesis: Functions to support master thesis

Description

Make a centered (scaled) genetic marker matrix

Usage

makeZ(M, bAlleleFrequency = NULL, scaled = TRUE, haploid = FALSE,
  SNPinRows = TRUE)

Arguments

M	matrix of genotypes in bi-allelic format (e.g. AA, AC, CC). Missing data is entered as NA.
bAlleleFrequency	vector of B allele frequencies for the markers. Default is NULL, which takes the column means of the M matrix or the column means divided by two in case of haplotypes.
scaled	logical whether scaling of genotype score need to be done. Default is TRUE.
haploid	logical wheter marker scores are haplotypes. Default is FALSE.
SNPinRows	logical whether markers are in rows. If FALSE markers are assumed to be present in columns. Default is TRUE.

Value

realization of the Z matrix in R matrix format

Examples

data(M)
head(makeZ(M))

digiYozhik/msc_thesis documentation built on May 14, 2019, 5:16 p.m.