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| <!-- badges: start --> | ||
| [](https://github.com/pbreheny/plmmr) | ||
| [](https://github.com/pbreheny/plmmr/actions) | ||
| [](https://app.codecov.io/gh/pbreheny/plmmr?branch=master) | ||
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| [](https://github.com/pbreheny/plmmr) [](https://github.com/pbreheny/plmmr/actions) [](https://app.codecov.io/gh/pbreheny/plmmr?branch=master) | ||
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| ## plmmr <img src="man/figures/plmmr_hex_sticker.png" align="right" alt="" width="150" /> | ||
| ## plmmr <img src="man/figures/plmmr_hex_sticker.png" align="right" width="150"/> | ||
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| The `plmmr` (**p**enalized **l**inear **m**ixed **m**odels in **R**) package contains functions that fit penalized linear mixed models to correct for unobserved confounding effects. | ||
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| ## Installation | ||
| ## Installation | ||
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| To install the latest version of the package: | ||
| To install the latest version of the package: | ||
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| ```r | ||
| ``` r | ||
| devtools::install_github("pbreheny/plmmr") | ||
| ``` | ||
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| For a description of the motivation of the functions in this package (along with examples) refer to the second module of [this GWAS data tutorial](https://pbreheny.github.io/adv-gwas-tutorial/index.html) | ||
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| ## Note on branches | ||
| ## So how fast is `plmmr`? And how well does it scale? | ||
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| To illustrate these important questions, I created a separate [GitHub repository](https://github.com/tabpeter/demo_plmmr/tree/master) that has all the scripts for a `plmmr` workflow using publicly-available genome-wide association (GWAS) data. The main takeaway: using GWAS data from a study with 1,400 samples and 800,000 SNPs, a full `plmmr` analysis will run in about half an hour using a single core on a laptop. | ||
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| Three smaller datasets ship with `plmmr`, and tutorials walking through how to analyze these data sets are documented in the [documentation site](https://pbreheny.github.io/plmmr/). While these datasets are useful for didactic purposes, they are not large enough to really highlight the computational scalability of `plmmr` -- this is what motivated the creation of the separate repository for a GWAS workflow. | ||
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| ## Note on branches | ||
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| The branches of this repo are organized in the following way: | ||
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| The branches of this repo are organized in the following way: | ||
| - `master` is the main (or 'head') branch. | ||
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| - `master` is the main (or 'head') branch. | ||
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| - `gh_pages` is where we are keeping all the documentation for `plmmr` | ||
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| - `gwas_scale` is an **archived** branch that contains the development version of the package I used to run my dissertation analysis. Will delete this eventually. | ||
| - `gh_pages` is where we are keeping all the documentation for `plmmr` | ||
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| - `gwas_scale` is an **archived** branch that contains the development version of the package I used to run my dissertation analysis. Will delete this eventually. |