mds.plink: Perform classical multidimensional scaling (MDS) with PLINK

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Perform classical multidimensional scaling (MDS) with PLINK

Usage

mds.plink(prefix, flags = "--autosome", K = 3, ...)

Arguments

prefix	a pointer to a PLINK fileset (of class plink)
flags	command-line flags passed directly to underlying PLINK call
K	project samples onto this many dimensions
...	ignored

Details

See the relevant PLINK documentation for details of the underlying calculations. The default is to perform MDS on autosomal genotypes only. Scaled eigenvalues (ie. percent variance explained by each dimension) are provided in attr(,"eigvals").

Value

a dataframe with individual IDs, family IDs, and then projections in columns "MDS1"..."MDSk".

References

PLINK v1.9: https://www.cog-genomics.org/plink2

Purcell S et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81(3): 559-575. doi:10.1086/519795.

See Also

pca.plink

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.