Converts and transforms data from GenomeStudio output into form that can be handled by the function snpmclust.
Usage
prepdata(rawdata)
Arguments
rawdata
Data frame taken from an import of GenomeStudio full data table.
Value
A list with the following components:
A list with the following components:
Details
prepdata expects a data frame that includes columns from an import of a GenomeStudio full data table. These columns include Name (the column of SNP rs-numbers) and the subcolumns Theta, R, GType, Score, X, Y, X.Raw, Y.Raw. Sample IDs are taken from the subcolumn prefixes. The data transformations in prepdata are an integral part of the SNPMClust
methodology.
References
Stephen W. Erickson, Joshua Callaway (2016). SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays. Journal of Statistical Software, 71(2), 1-9. doi:10.18637/jss.v071.c02