# swfdr Science-wide false discovery rate `swfdr` is an R package for dealing with multiple hypothesis testing. ## Installation The package is available through Bioconductor. ``` library(BiocManager) BiocManager::install("swfdr") ``` It is also possible to install in-development versions from github. ``` library(devtools) install_github("leekgroup/swfdr") ``` ## Example A minimal working example for using the `lm_pi0` and `lm_qvalue` functions is as follows ``` library(swfdr) x <- c(rbeta(1000, 0.2, 1), runif(1000, 0, 1)) x.covariate = rep(c(1,2), each=1000) # compute covariate-adjusted pi0 - probability of null hypothesis to be true x.pi0 = lm_pi0(x, X=x.covariate) x.pi0 # compute covariate-adjusted qvalues x.qvalues <- lm_qvalue(x, X=x.covariate) x.qvalues ```