## ----echo=FALSE, include=FALSE------------------------------------------------ library(knitr) knitr::opts_chunk$set( warning=FALSE, message=FALSE ) ## ----------------------------------------------------------------------------- library(dplyr) library(ppcseq) ## ----eval=FALSE--------------------------------------------------------------- # fileConn<-file("~/.R/Makevars") # writeLines(c( "CXX14FLAGS += -O3","CXX14FLAGS += -DSTAN_THREADS", "CXX14FLAGS += -pthread"), fileConn) # close(fileConn) ## ----eval=FALSE--------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("ppcseq") ## ----------------------------------------------------------------------------- data("counts") counts ## ----warning=FALSE, message=FALSE,results='hide'------------------------------ # Import libraries if(Sys.info()[['sysname']] == "Linux") counts.ppc = counts %>% mutate(is_significant = FDR < 0.0001) %>% identify_outliers( formula = ~ Label, .sample = sample, .transcript = symbol, .abundance = value, .significance = PValue, .do_check = is_significant, percent_false_positive_genes = 5, approximate_posterior_inference = FALSE, cores = 1, # This is ONLY for speeding up the Vignette execution draws_after_tail = 1 ) ## ----------------------------------------------------------------------------- if(Sys.info()[['sysname']] == "Linux") counts.ppc ## ----------------------------------------------------------------------------- if(Sys.info()[['sysname']] == "Linux") counts.ppc_plots = counts.ppc %>% plot_credible_intervals() ## ----------------------------------------------------------------------------- if(Sys.info()[['sysname']] == "Linux") counts.ppc_plots %>% pull(plot) %>% .[seq_len(1)] ## ----softwareinfo------------------------------------------------------------- sessionInfo()