MDS constraint: --mds-cluster, --within

[davidonlaptop]

Description

This feature adds the --mds-cluster and --within constraint(s) on the --mds-plot option described in issue #17. For more info, check: http://pngu.mgh.harvard.edu/~purcell/plink/mds.shtml#options

Analysis

Add a comment to this issue with:

• plink version used as reference (1.07 or 1.90 beta 3)
• relevant C++ function name(s) and the file name(s) where they appear
• Document the algorithm and/or mathematical formula to compute:
  • --mds-cluster option
  • --within option

Design

Add a comment to this issue describing how this will be implemented in Spark, and how it differs from plink.

Implementation

The implementation should use:

• Scala
• Spark RDD
• Spark MLlib / GraphX (if appropriate)