Short Tutorials

This section presents some short tutorials describing the functionality of the genipe module. The first one describes the genome-wide imputation pipeline itself. The other tutorials describe provided tools to perform statistical analysis or data management.

  1. Pipeline tutorial
  2. Linear mixed effects tutorial
  3. Survival tutorial
  4. SKAT tutorial
  5. Linear tutorial
  6. Logistic tutorial
  7. Site extraction tutorial

Pipeline tutorial

This tutorial is a walk-through the main objective of this module, which is the genome-wide imputation of genotypes. It describes in detail the expected input and output files.

Linear mixed effects tutorial

This tutorial is a walk-through of a linear mixed effects analysis for repeated measurements. It describes in detail the expected input and output files.

Survival tutorial

This tutorial is a walk-through of a typical survival analysis (using Cox’s proportional hazard model). It describes in detail the expected input and output files.

SKAT tutorial

This tutorial is a walk-through of a typical SKAT analysis and describes the expected input and output files.

Linear tutorial

This tutorial is a walk-through of a linear regression analysis (using ordinary least squares). It describes in detail the expected input and output files.

Logistic tutorial

This tutorial is a walk-through of a logistic regression analysis (using a GLM with a binomial distribution and a logit link). It describes in detail the expected input and output file.

Site extraction tutorial

This tutorial is a walk-through of the tool used to extract sites from imputation files. It describes in detail the expected input and output file.