HardyWeinberg: MakeFactor – R documentation

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MakeFactor

Make factors from genotyping data

Description

MakeFactor converts bi-allelic genetic marker data, whether coded numerically as (0,1,2) or as (GG,GT,TT), etc. into standard factors coded as AA, AB, BB.

Usage

MakeFactor(x, coding = c(0, 1, 2))

Arguments

`x`	A vector containing genotyping results
`coding`	Describes the numerical coding of the genotype data in order AA, AB and BB. Only relevant if `x` is numerical

Details

If x is a factor, it will be coerced to a factor with levels AA, AB and BB. Important detail: the produced factors will have only those levels that are observed in the data. E.g., if genotyping results only consist of (0,1), then the resulting factor will not have level BB (which would be an empty category)

Value

A factor variable

Author(s)

Jan Graffelman jan.graffelman@upc.edu

Examples

y <- c(1,1,0,0,2,2)
data.frame(y,MakeFactor(y))

y <- c(2,2,3,3,1,1)
data.frame(y,MakeFactor(y,coding=c(1,2,3)))

data(Markers)
data.frame(Markers[,1],MakeFactor(Markers[,1],coding=c(1,2,3)))

HardyWeinberg

Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

v1.7.2

GPL (>= 2)

Authors

Jan Graffelman [aut, cre], Christopher Chang [ctb], Xavi Puig [ctb], Jan Wigginton [ctb], Leonardo Ortoleva [ctb], William R. Engels [ctb]

Initial release

2021-04-28