GELOG / adam-ibs

Ports the IBS/MDS/IBD functionality of Plink to Spark / ADAM

Apache License 2.0

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missinIBS clustering constraint: g genotype data (--ibm) #12

Open davidonlaptop opened 9 years ago

davidonlaptop commented 9 years ago

Description

This feature adds the --ibm constraint(s) on the --cluster option described in issue #7. For more info, check: http://pngu.mgh.harvard.edu/~purcell/plink/strat.shtml#options

The input file is the model created in #3.

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 structure of the hh file generated by plink (not always present).
Document the algorithm and/or mathematical formula to compute:
- --ibm 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)