diff --git a/README.Rmd b/README.Rmd deleted file mode 100644 index 7eff48b1267d6b473845d288611c79aa60e3ad02..0000000000000000000000000000000000000000 --- a/README.Rmd +++ /dev/null @@ -1,97 +0,0 @@ -# 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 link) - -## Prerequisite - -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: - -```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: - + 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 tested allele of the variant - + the frequency of the allele A0 - + the regression coefficient of the main genetic effect - + the regression coefficient of the interaction effect - -```{r, echo = FALSE} -data("GWAS") -print(GWAS, row.names = FALSE) -``` - -* 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 - + the standard deviation of the phenotype in the cohort - + the exposure mean in the cohort - + the standard deviation of the exposure in the cohort - -```{r, echo = FALSE} -data("COHORT") -print(COHORT, row.names = FALSE) -``` - -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) - -# Load the meta-analysis summary statistics file -data(GWAS) - -# Load the cohort description file -data(COHORT) - -# Compute the genotype correlation matrix from the reference panel -C <- getGenoCorMatrix(GWAS$RSID, GWAS$CHR, GWAS$POS, GWAS$A0, "EUR", pruning = FALSE) - -# Make sure SNPs in the GWAS data and in the correlation matrix match -# Necessary if pruning = TRUE, otherwise should have no effect -GWAS <- checkInput(GWAS, colnames(C)) - -# Retrieve mean and variance of the exposure and the phenotype -# from individual cohort summary statistics -parsY <- calculateParamsFromIndParams(COHORT$PHENO_N, COHORT$PHENO_Mean, COHORT$PHENO_SD) -parsE <- calculateParamsFromIndParams(COHORT$PHENO_N, COHORT$EXPO_Mean, COHORT$EXPO_SD) - -# Re-scale effect sizes as if estimated in a standardized model -std_betaG <- standardizeBeta(GWAS$MAIN_EFFECT, GWAS$INT_EFFECT, GWAS$FREQ_A0, parsE[1], parsE[2], type = "G") -std_betaI <- standardizeBeta(GWAS$MAIN_EFFECT, GWAS$INT_EFFECT, GWAS$FREQ_A0, parsE[1], parsE[2], type = "I") - -# Estimation of the fraction of variance explained -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 - -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://github.com/vincenla/VarExp/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://github.com/vincentla/VarExp/) file for details \ No newline at end of file