CLARITE Documentation

Version:1.1.1.post47+g0530ed3

CLeaning to Analysis: Reproducibility-based Interface for Traits and Exposures

• Hall Lab Homepage
• CLARITE Github Repo
• Motivation
• Installation
  • Basic Install
  • Running R code from CLARITE
• Citing CLARITE
• Usage
  • Organization of Functions
  • Coding Style
• Example Analysis
  • Load Data
  • Define the phenotype and covariates
  • Initial cleanup / variable selection
  • QC
  • Checking the phenotype distribution
  • EWAS
  • Replication
  • Manhattan Plots
• Complex Survey Data
  • Single Clusters
  • Missing Weights
  • Subsets
• Regression
  • Regression Classes

API Reference

If you are looking for information on a specific function, class or method, this part of the documentation is for you.

• API Reference
  • Analyze
  • Describe
  • Load
  • Modify
  • Plot
  • Survey

CLI Reference

Documentation for using the CLI

• CLI Reference
  • –skip and –only
  • Commands

Additional Notes

Release History, etc

• Release History
  • v1.1.1 (2020-06-12)
  • v1.1.0 (2020-08-14)
  • v1.0.1 (2020-06-12)
  • v1.0.0 (2020-06-04)
  • v0.10.0 (2020-05-28)
  • v0.9.1 (2019-11-20)
  • v0.9.0 (2019-10-31)
  • v0.8.0 (2019-09-03)
  • v0.7.0 (2019-07-23)
  • v0.6.0 (2019-07-11)
  • v0.5.0 (2019-06-28)
  • v0.4.0 (2019-06-18)
  • v0.3.0 (2019-05-31)
  • v0.2.1 (2019-05-02)
  • v0.2.0 (2019-04-30)
  • v0.1.0 (2019-04-23)