HardyWeinberg: HWClrPlot – R documentation

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HWClrPlot

Plot genetic markers in centred log-ratio coordinates

Description

HWClrPlot creates a scatter plot of the centred log-ratio coordinates of bi-allelic genetic markers. Hardy-Weinberg equilibrium is indicated by a straigh line in the plot.

Usage

HWClrPlot(X, zeroadj = 0.5)

Arguments

`X`	A matrix of genotype counts (columns AA, AB, BB)
`zeroadj`	Zero-adjustment parameter. Zero counts in the count matrix are substituted by `zeroadj` which is 0.5 by default.

Value

NULL

Author(s)

Jan Graffelman (jan.graffelman@upc.edu)

References

Graffelman, J. and Egozcue, J. J. (2011) Hardy-Weinberg equilibrium: a non-parametric compositional approach. In: Vera Pawlowsky-Glahn and Antonella Buccianti (eds.) Compositional Data Analysis: Theory and Applications, John Wiley \& Sons, Ltd, pp. 207-215

Examples

X <- HWClo(HWData(100,100))
   HWClrPlot(X)

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