Short Tutorials ================ This section presents some short tutorials describing the functionality of the :py:mod:`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. :ref:`genipe-tut` 2. :ref:`mixedlm-tut` 3. :ref:`cox-tut` 4. :ref:`skat-tut` 5. :ref:`linear-tut` 6. :ref:`logistic-tut` 7. :ref:`extraction-tut` .. _genipe-tut: 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. .. toctree:: :maxdepth: 2 tutorials/tutorial_genipe .. _mixedlm-tut: 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. .. toctree:: :maxdepth: 2 tutorials/tutorial_mixedlm .. _cox-tut: 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. .. toctree:: :maxdepth: 2 tutorials/tutorial_cox .. _skat-tut: SKAT tutorial -------------- This tutorial is a walk-through of a typical SKAT analysis and describes the expected input and output files. .. toctree:: :maxdepth: 2 tutorials/tutorial_SKAT .. _linear-tut: 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. .. toctree:: :maxdepth: 2 tutorials/tutorial_linear .. _logistic-tut: 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. .. toctree:: :maxdepth: 2 tutorials/tutorial_logistic .. _extraction-tut: 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. .. toctree:: :maxdepth: 2 tutorials/tutorial_extract