## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown() ## ----------------------------------------------------------------------------- ## load package library(HarmanData) data(IMR90) data(NPM) data(OLF) data(Infinium5) olf.data[1:5, 1:5] dim(olf.data) table(olf.info) ## ----------------------------------------------------------------------------- ## load package library(HarmanData) data(Infinium5) lvr.harman["cg01381374", ] md.harman["cg01381374", ] ## ----------------------------------------------------------------------------- library(Harman) data(episcope) bad_batches <- c(1, 5, 9, 17, 25) is_bad_sample <- episcope$pd$array_num %in% bad_batches myK <- discoverClusteredMethylation(episcope$original[, !is_bad_sample]) mykClust = kClusterMethylation(episcope$original, row_ks=myK) res = clusterStats(pre_betas=episcope$original, post_betas=episcope$harman, kClusters = mykClust) all.equal(episcope$ref_md$meandiffs_harman, res$meandiffs) all.equal(episcope$ref_lvr$var_ratio_harman, res$log2_var_ratio)