Overview

The R-Package "AIPS" is to infer ancestry membership using a distance-based analysis to account for geogenetic subpopulation structure.


1. Principal Component Analysis and Spatial Analysis using Ancestry Informative Markers

  • AIPS-PCA.R computes the PC scores on predefined ancestry informative markers.

  • AIPS-AI.R calculates centroids from ancestry known subpopulations and infer the ancestry membership using pairwise distance between each entroid and individual.

  • EURO7SubPOP.txt Table for 7 European subpopulations.

  • EURO-Known-SampleIndex.txt 952 known European sample index.


    2. Instruction

  • AIPS Manual is the documentation for how to run "AIPS-PCA.R" and "AIPS-AI.R".


    3. Reference Data

  • fam file includes 952 samples on 25732 AIMs in plink binary format.

  • bed file includes 952 samples on 25732 AIMs in plink binary format.

  • bim file includes 952 samples on 25732 AIMs in plink binary format.

  • fam file includes 4,376 samples including 952 known samples on 25732 AIMs in plink binary format.

  • bed file includes 4,376 samples including 952 known samples on 25732 AIMs in plink binary format.

  • bim file includes 4,376 samples including 952 known samples on 25732 AIMs in plink binary format.


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