diff --git a/.gitignore b/.gitignore index 5b6a0652566d10360493952aec6d4a4febc77083..3e2e76369f65d3f9dd008f77e90be904b061ed13 100644 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,4 @@ .Rhistory .RData .Ruserdata +VarExp.Rproj diff --git a/README.Rmd b/README.Rmd index 4c252ff7712664decd88ffef47fab510826d3e84..8309e3daadb82bd0414e5c892785ac1376c188c4 100644 --- a/README.Rmd +++ b/README.Rmd @@ -7,12 +7,16 @@ knitr::opts_chunk$set(echo = TRUE) The R package **VarExp** provides functions for the estimating of the percentage of phenotypic variance explained by genetic effects, interaction effects or jointly by both effects. This suite of functions are useful for meta-analysis designs where pooling individual genotype data is challenging. A pre-print article related to this work is available [here](bioRkiv link) +## Prerequisite + +Library [**Rcurl**](https://cran.r-project.org/web/packages/RCurl/index.html) is required to run **VarExp** + ## Installation -Install the development version of **VarExp** from GitHub by typing: +For now, **VarExp** can be installed only using package source. In R, after setting your working directory to *VarExp_0.1.0.tar.gz* location, type: ```r -devtools::install_github("vincela/VarExp") +install.packages("VarExp_0.1.0.tar.gz", repos = NULL, type = "source") ``` ## Input format @@ -55,7 +59,7 @@ Data used in this tutorial are included in the ***VarExp*** package. ```r # Load the package -library(VarExp2) +library(VarExp) # Load the meta-analysis summary statistics file data(GWAS) diff --git a/README.html b/README.html index abdef278096e0d176d345a6670a0d0375a72d9b7..e363729acaa01c7bbc0bd03c1f8b6ce7edd4e1c2 100644 --- a/README.html +++ b/README.html @@ -122,10 +122,14 @@ $(document).ready(function () { <div id="varexp" class="section level1"> <h1>VarExp</h1> <p>The R package <strong>VarExp</strong> provides functions for the estimating of the percentage of phenotypic variance explained by genetic effects, interaction effects or jointly by both effects. This suite of functions are useful for meta-analysis designs where pooling individual genotype data is challenging. A pre-print article related to this work is available <a href="bioRkiv%20link">here</a></p> +<div id="prerequisite" class="section level2"> +<h2>Prerequisite</h2> +<p>Library <a href="https://cran.r-project.org/web/packages/RCurl/index.html"><strong>Rcurl</strong></a> is required to run <strong>VarExp</strong></p> +</div> <div id="installation" class="section level2"> <h2>Installation</h2> -<p>Install the development version of <strong>VarExp</strong> from GitHub by typing:</p> -<pre class="r"><code>devtools::install_github("vincela/VarExp")</code></pre> +<p>For now, <strong>VarExp</strong> can be installed only using package source. In R, after setting your working directory to <em>VarExp_0.1.0.tar.gz</em> location, type:</p> +<pre class="r"><code>install.packages("VarExp_0.1.0.tar.gz", repos = NULL, type = "source")</code></pre> </div> <div id="input-format" class="section level2"> <h2>Input format</h2> @@ -176,7 +180,7 @@ $(document).ready(function () { <h2>Short tutorial</h2> <p>Data used in this tutorial are included in the <strong><em>VarExp</em></strong> package.</p> <pre class="r"><code># Load the package -library(VarExp2) +library(VarExp) # Load the meta-analysis summary statistics file data(GWAS) @@ -211,7 +215,11 @@ fracJ <- calculateVarFrac(std_betaG, std_betaI, C, parsY[2], sum(COHORT$PH </div> <div id="code-of-conduct" class="section level2"> <h2>Code of conduct</h2> -<p>Please note that this project is released with a <a href="link%20to%20file">Contributor Code of Conduct</a>. By participating in this project you agree to abide by its terms.</p> +<p>Please note that this project is released with a <a href="https://github.com/vincenla/VarExp/code-of-conduct.md">Contributor Code of Conduct</a>. By participating in this project you agree to abide by its terms.</p> +</div> +<div id="license" class="section level2"> +<h2>License</h2> +<p>This project is licensed under the MIT License - see the <a href="https://github.com/vincentla/VarExp/">LICENSE.md</a> file for details</p> </div> </div> diff --git a/man/COHORT.Rd b/man/COHORT.Rd index 2c8f247b2147ffb60cfa8db8e119755b572dce07..539c74234c6c741507c3327723ecb5a61f21690f 100644 --- a/man/COHORT.Rd +++ b/man/COHORT.Rd @@ -4,7 +4,7 @@ \name{COHORT} \alias{COHORT} \title{Example of cohort description input file} -\format{An object of class \code{data.frame} with 5 rows and 7 columns.} +\format{An object of class \code{data.frame} with 5 rows and 6 columns.} \usage{ COHORT } diff --git a/man/GWAS.Rd b/man/GWAS.Rd index 378be4035b5b8d7899ceb69b8ca6f34a552dfbf7..a9788203f471e000e829978e887224637578bb50 100644 --- a/man/GWAS.Rd +++ b/man/GWAS.Rd @@ -4,7 +4,7 @@ \name{GWAS} \alias{GWAS} \title{Example of GWAS result input file} -\format{An object of class \code{data.frame} with 15 rows and 13 columns.} +\format{An object of class \code{data.frame} with 10 rows and 7 columns.} \usage{ GWAS }