## ----style-knitr, eval=TRUE, echo=FALSE, results="asis"-------------------- BiocStyle::latex() ## ----lib-load, message=FALSE----------------------------------------------- library(quantro) ## ----data-load, message=FALSE---------------------------------------------- library(quantro) 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()