## ----echo=FALSE, results="hide", message=FALSE-------------------------------- require(knitr) opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE) ## ----style, echo=FALSE, results='asis'---------------------------------------- BiocStyle::markdown() ## ----install-quantro---------------------------------------------------------- if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("quantro") ## ----lib-load, message=FALSE-------------------------------------------------- library(quantro) ## ----data-load, message=FALSE------------------------------------------------- library(minfi) data(flowSorted) p <- getBeta(flowSorted, offset = 100) pd <- pData(flowSorted) dim(p) head(pd) ## ----plot-distributions-density, fig.height=5, fig.width=6-------------------- matdensity(p, groupFactor = pd$CellType, xlab = " ", ylab = "density", main = "Beta Values", brewer.n = 8, brewer.name = "Dark2") legend('top', c("NeuN_neg", "NeuN_pos"), col = c(1, 2), lty = 1, lwd = 3) ## ----plot-distributions-boxplot, fig.height=5, fig.width=6-------------------- matboxplot(p, groupFactor = pd$CellType, xaxt = "n", main = "Beta Values") ## ----calculate-quantro1------------------------------------------------------- qtest <- quantro(object = p, groupFactor = pd$CellType) qtest ## ----quantro-summary---------------------------------------------------------- summary(qtest) ## ----quantro-medians---------------------------------------------------------- anova(qtest) ## ----quantro-quantroStat------------------------------------------------------ quantroStat(qtest) ## ----flowSorted-fullEx-------------------------------------------------------- is(flowSorted, "MethylSet") qtest <- quantro(flowSorted, groupFactor = pData(flowSorted)$CellType) qtest ## ----quantro-parallel--------------------------------------------------------- library(doParallel) registerDoParallel(cores=1) qtestPerm <- quantro(p, groupFactor = pd$CellType, B = 1000) qtestPerm ## ----quantro-plot, fig.height=5, fig.width=6---------------------------------- quantroPlot(qtestPerm) ## ----sessionInfo, results='markup'-------------------------------------------- sessionInfo()