{"id":19644885,"url":"https://github.com/uscbiostats/fdrci","last_synced_at":"2025-07-22T23:34:27.014Z","repository":{"id":29916592,"uuid":"122653195","full_name":"USCbiostats/fdrci","owner":"USCbiostats","description":"Permutation-Based FDR Point and Confidence Interval Estimation","archived":false,"fork":false,"pushed_at":"2022-10-17T23:50:12.000Z","size":395,"stargazers_count":3,"open_issues_count":2,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-28T14:45:24.949Z","etag":null,"topics":["permutation-test","r-package","rstats"],"latest_commit_sha":null,"homepage":"https://uscbiostats.github.io/fdrci","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/USCbiostats.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2018-02-23T17:40:15.000Z","updated_at":"2023-02-14T09:44:42.000Z","dependencies_parsed_at":"2023-01-14T15:54:33.168Z","dependency_job_id":null,"html_url":"https://github.com/USCbiostats/fdrci","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/USCbiostats/fdrci","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/USCbiostats%2Ffdrci","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/USCbiostats%2Ffdrci/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/USCbiostats%2Ffdrci/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/USCbiostats%2Ffdrci/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/USCbiostats","download_url":"https://codeload.github.com/USCbiostats/fdrci/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/USCbiostats%2Ffdrci/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266590679,"owners_count":23952981,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-07-22T02:00:09.085Z","response_time":66,"last_error":null,"robots_txt_status":null,"robots_txt_updated_at":null,"robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["permutation-test","r-package","rstats"],"created_at":"2024-11-11T14:30:34.696Z","updated_at":"2025-07-22T23:34:26.996Z","avatar_url":"https://github.com/USCbiostats.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n[![Travis build status](https://travis-ci.org/USCbiostats/fdrci.svg?branch=master)](https://travis-ci.org/USCbiostats/fdrci)\n\n[![Build status](https://ci.appveyor.com/api/projects/status/jykjw0b9f5rc9g7w?svg=true)](https://ci.appveyor.com/project/gvegayon/fdrci)\n\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r setup, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n# fdrci\n\n\u003e FDR functions for permutation-based estimators, including pi0 as well as FDR\n             confidence intervals. The confidence intervals account for dependencies between\n             tests by the incorporation of an overdispersion parameter, which is estimated\n             from the permuted data. --- From the package description\n\n## Installation\n\nYou can install fdrci from GitHub with:\n\n```{r gh-installation, eval = FALSE}\n# install.packages(\"devtools\")\ndevtools::install_github(\"USCbiostats/fdrci\")\n```\n\n## Example\n\nThis is a basic example which shows you how to solve a common problem:\n\n```{r example}\nlibrary(fdrci)\n\nss = 100\nnvar = 100\nX = as.data.frame(matrix(rnorm(ss*nvar),nrow=ss,ncol=nvar))\nY = as.data.frame(matrix(rnorm(ss*nvar),nrow=ss,ncol=nvar))\nnperm = 10\n\nmyanalysis = function(X,Y){\n\tntests = ncol(X)\n\trslts = as.data.frame(matrix(NA,nrow=ntests,ncol=2))\n\tnames(rslts) = c(\"ID\",\"pvalue\")\n\trslts[,\"ID\"] = 1:ntests\n\tfor(i in 1:ntests){\n\t\tfit = cor.test(X[,i],Y[,i],na.action=\"na.exclude\",\n\t\t\talternative=\"two.sided\",method=\"pearson\")\n\t\trslts[i,\"pvalue\"] = fit$p.value\n\t}\n\treturn(rslts)\n} # End myanalysis\n\n# Generate observed results\nobs = myanalysis(X,Y)\n\n# Generate permuted results\nperml = vector('list',nperm)\nfor(p_ in 1:nperm){\n\tX1 = X[order(runif(nvar)),]\n\tperml[[p_]] = myanalysis(X1,Y)\n}\n\n# FDR results table\nmyfdrtbl = fdrTbl(obs$pvalue,perml,\"pvalue\",nvar,0.5,3)\nmyfdrtbl1 = fdrTbl(obs$pvalue,perml,\"pvalue\",n.col,0.5,3,correct=\"BH\")\nfdrTbl(obs$pvalue, NULL, \"pvalue\",n.col,0.5,3,meff = TRUE, seff = TRUE, mymat = X, nperms = 5)\n\n# Plot results\nFDRplot(myfdrtbl,0,3,annot=\"A. An Example\")\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fuscbiostats%2Ffdrci","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fuscbiostats%2Ffdrci","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fuscbiostats%2Ffdrci/lists"}