## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----getPackage, eval=FALSE--------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("PAIRADISE") ## ----getDevel, eval=FALSE----------------------------------------------------- # BiocManager::install("hubentu/PAIRADISE") ## ----Load, message=FALSE------------------------------------------------------ library(PAIRADISE) ## ----------------------------------------------------------------------------- library(abind) icount <- matrix(1:4, 1) scount <- matrix(5:8, 1) acount <- abind(icount, scount, along = 3) acount design <- data.frame(sample = rep(c("s1", "s2"), 2), group = rep(c("T", "N"), each = 2)) lens <- data.frame(sLen=1L, iLen=2L) PDseDataSet(acount, design, lens) ## ----------------------------------------------------------------------------- data("sample_dataset") sample_dataset ## ----------------------------------------------------------------------------- data("sample_dataset_CEU") data("sample_dataset_LUSC") ## ----------------------------------------------------------------------------- pdat <- PDseDataSetFromMat(sample_dataset) pdat ## ----------------------------------------------------------------------------- pairadise_output <- pairadise(pdat, numCluster = 2) ## ----------------------------------------------------------------------------- res <- results(pairadise_output, p.adj = "BH", sig.level = 0.01) res ## ----------------------------------------------------------------------------- res <- results(pairadise_output, details = TRUE) colnames(res) res$latent[3,] ## ----------------------------------------------------------------------------- sessionInfo()