NEW README

README.md

 VarExp
 ======
 
-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%20link)
+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%20link)
 
 Prerequisite
 ------------
 
-Library
-[**Rcurl**](https://cran.r-project.org/web/packages/RCurl/index.html) is
-required to run **VarExp**
+Library [**Rcurl**](https://cran.r-project.org/web/packages/RCurl/index.html) is required to run **VarExp**
 
 Installation
 ------------
 
-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:
+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
 install.packages("VarExp_0.1.0.tar.gz", repos = NULL, type = "source")
+```
 
 Input format
 ------------
 
 Two input files are required.
 
--   A file providing the meta-analysis results with the following
-    mandatory columns:
+-   A file providing the meta-analysis results with the following mandatory columns:
     -   the rs identifier of the variant
     -   the chromosome number on which the variant is
-    -   the physical position of the variant (currently in NCBI Build
-        B37)
+    -   the physical position of the variant (currently in NCBI Build B37)
     -   the tested allele of the variant
     -   the frequency of the allele A0
     -   the regression coefficient of the main genetic effect
@@ -54,9 +45,7 @@ Two input files are required.
     ##   rs7538305   1  824398  C 0.15379  0.054950590 -0.04494799
     ##  rs28613513   1 1112810  T 0.05358 -0.001334013  0.10294423
 
--   A file providing the summary statistics for the outcome and the
-    exposure in each individual cohort included in the meta-analysis.
-    Mandatory columns of this file are:
+-   A file providing the summary statistics for the outcome and the exposure in each individual cohort included in the meta-analysis. Mandatory columns of this file are:
     -   the identifier of the cohort
     -   the sample size of the cohort
     -   the phenotype mean in the cohort
@@ -73,15 +62,14 @@ Two input files are required.
     ##       4   10000   1.342020 3.151429  1.999943 1.256718
     ##       5   10000   1.385564 3.153274  2.002401 1.235129
 
-Note that in the case of a binary exposure, the two latter columns can
-be replaced by a single column providing the count of exposed
-individuals in each cohort.
+Note that in the case of a binary exposure, the two latter columns can be replaced by a single column providing the count of exposed individuals in each cohort.
 
 Short tutorial
 --------------
 
 Data used in this tutorial are included in the ***VarExp*** package.
 
+``` r
 # Load the package
 library(VarExp)
 
@@ -111,6 +99,7 @@ Data used in this tutorial are included in the ***VarExp*** package.
 fracG    <- calculateVarFrac(std_betaG, std_betaI, C, parsY[2], sum(COHORT$PHENO_N), "G")
 fracI    <- calculateVarFrac(std_betaG, std_betaI, C, parsY[2], sum(COHORT$PHENO_N), "I")
 fracJ    <- calculateVarFrac(std_betaG, std_betaI, C, parsY[2], sum(COHORT$PHENO_N), "J")
+```
 
 Bug report / Help
 -----------------
@@ -120,13 +109,9 @@ Please open an issue if you find a bug.
 Code of conduct
 ---------------
 
-Please note that this project is released with a [Contributor Code of
-Conduct](https://gitlab.pasteur.fr/statistical-genetics/VarExp/blob/master/code-of-conduct.md).
-By participating in this project you agree to abide by its terms.
+Please note that this project is released with a [Contributor Code of Conduct](https://gitlab.pasteur.fr/statistical-genetics/VarExp/blob/master/code-of-conduct.md). By participating in this project you agree to abide by its terms.
 
 License
 -------
 
-This project is licensed under the MIT License - see the
-[LICENSE.md](https://gitlab.pasteur.fr/statistical-genetics/VarExp/blob/master/LICENSE)
-file for details
+This project is licensed under the MIT License - see the [LICENSE.md](https://gitlab.pasteur.fr/statistical-genetics/VarExp/blob/master/LICENSE) file for details