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.
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.