createBins: Bin CN data

In mknoll/cnAnalysis450k: Copy Number Analysis for 450k Illumina Methylation Arrays

Description

Calculate mean, median, sd for each bin for a given binsize.

Usage

createBins(data, ctrl, ctrlAll, statistic = "wilcoxon", binsize = 2e+05,
  output = "diff", arrayType = "auto", noCores = -1)

Arguments

data	sample data
ctrl	control data
ctrlAll	CN data of all control samples
statistic	statistics test to compare groups (controls vs smp); "t.test" or "wilcoxon" (Mann-Whitney-U Test)
binsize	binsize
output	"ratio" (Sample/Ctrl) or "diff" (Sample-Ctrl)
arrayType	"auto","450k", "EPIC"; auto -> tries to automatically determine the array type (450k, EPIC)
noCores	number of cores for parallelization: needed to pass the cran examples :/

Value

bins with their corresponding value

Examples

data <- minfi::getCN(minfi::preprocessRaw(minfiData::RGsetEx))
ctrlAll <- data[,4,drop=FALSE]
ctrl <- data[,5] # apply(ctrlAll, 1, "median")
data <- data[,1,drop=FALSE]
createBins(data,ctrl,ctrlAll, binsize=50000000, noCores=2)[1:3,]

mknoll/cnAnalysis450k documentation built on May 23, 2019, 2:01 a.m.