## ----eval=FALSE--------------------------------------------------------------- # install.packages("BiocManager") # BiocManager::install("SCBN") ## ----------------------------------------------------------------------------- library(SCBN) ## ----------------------------------------------------------------------------- data(orthgenes) orthgenes[, 6:9] <- round(orthgenes[, 6:9]) orthgenes1 <- orthgenes[!(is.na(orthgenes[,6])|is.na(orthgenes[,7])| is.na(orthgenes[,8])|is.na(orthgenes[,9])), ] sim_data <- generateDataset(commonTags=5000, uniqueTags=c(100, 300), unmapped=c(400, 200),group=c(1, 2), libLimits=c(.9, 1.1)*1e6, empiricalDist=orthgenes1[, 6], genelength=orthgenes1[, 2], randomRate=1/100, pDifferential=.05, pUp=.5, foldDifference=2) ## ----------------------------------------------------------------------------- data(orthgenes) head(orthgenes) ## ----------------------------------------------------------------------------- data(sim_data) head(sim_data) ## ----------------------------------------------------------------------------- data(sim_data) factor <- SCBN(orth_gene=sim_data, hkind=1:1000, a=0.05) factor ## ----------------------------------------------------------------------------- data(sim_data) orth_gene <- sim_data hkind <- 1:1000 scale <- factor$scbn_val x <- orth_gene[, 2] y <- orth_gene[, 4] lengthx <- orth_gene[, 1] lengthy <- orth_gene[, 3] n1 <- sum(x) n2 <- sum(y) p_value <- sageTestNew(x, y, lengthx, lengthy, n1, n2, scale) head(p_value)