Git Product home page Git Product logo

pca_for_gwas_data's Introduction

PCA_for_GWAS_data

Features

  • PCA for GWAS data
  • できるだけnumpy以外のライブラリを使わないで実装してみる

Installation

  • numpy
  • pandas

USAGE

  1. plink形式でGWASデータを取得
  2. pedファイルから、SNPのデータを切り出す
  3. 頻度に基づき、ATGCに0か1を割り当て、ホモ:0 or 2、ヘテロ:1とする ー＞ 人数 x SNP数のマトリクスを得る：SNP_data.npz
  4. PCA.pyを用いて、PCAを実行する （比較のために、scikit-learnを用いたPCAも用意しています: PCA_sklearn.py）

pca_for_gwas_data's People

Contributors

dsatoh20 avatar

Watchers

avatar

pca_for_gwas_data's Issues

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.