inst/testData/testData_compartments.R

In minfi: Analyze Illumina Infinium DNA methylation arrays

library(minfiData)
library(digest)

GMsetEx <- mapToGenome(MsetEx)
gr.cor <- createCorMatrix(GMsetEx, res=500*1000)
set.seed(456)
gr.ab <- extractAB(gr.cor)

digest_compartments <- list(cor.matrix = minfi:::.digestMatrix(gr.cor$cor.matrix),
                           pc = minfi:::.digestVector(gr.ab$pc, digits = 2))
save(digest_compartments, file = "../unitTests/digest_compartments.rda")

sessionInfo()
rm(list = ls())

# ------------------------------------------------------------------------------
# DelayedArray tests
#

library(DelayedArray)

assays(MsetEx) <- endoapply(assays(MsetEx), DelayedArray)

GMsetEx <- mapToGenome(MsetEx)
gr.cor <- createCorMatrix(GMsetEx, res=500*1000)
set.seed(456)
gr.ab <- extractAB(gr.cor)

digest_compartments <- list(cor.matrix = minfi:::.digestMatrix(gr.cor$cor.matrix),
                            pc = minfi:::.digestVector(gr.ab$pc, digits = 2))
save(digest_compartments, file = "../unitTests/digest_compartments.DelayedArray.rda")

sessionInfo()
rm(list = ls())