geno_012: Marker scores into 0, 1, 2 format
In vincentgarin/GWASToolBox: GWAS analysis

Description Usage Arguments Value Author(s) Examples

Transform genotype marker score into 0, 1, 2 format. The score represents the number of copies of the allele with the lowest marker allele frequency (MAF).

1	geno_012(mk.mat)

mk.mat

Character genotype marker score matrix. Marker scores must be coded using one letter for each allele. For example, AA, CC, GG, TT, AC, AG, AT, CA, CG, CT, GA, GC, GT, TA, TC, TG. Missing values must be coded NA.

Return:

List with two matrices

`geno012`	Marker `matrix` with marker scores coded as 0, 1, 2 corresponding to the number of copies of the least frequent SNP allele.
`all.ref`	`matrix` with reference allele scores. The first row represents the allele with the highest MAF, the second the one with the lowest MAF and the two others the heterozygous scores.

Vincent Garin