runConumee: Analyze data with conumee

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

Description

Analyzes the given 450k data with conumee, extracting either segments, bins or transcripts.

Usage

runConumee(data, ctrl, what = "segments", tx = NULL)

Arguments

data	MethylSet: sample data
ctrl	MethylSet: reference
what	type of return data: segments, bins, transcripts
tx	vector of transcripts of interests

Value

list with $data and $what, containing the CNV.write conumee outputs

Examples

print("A runnable example is also shown in the 
createConumeeMatrix examples")
#require(IlluminaHumanMethylation450kanno.ilmn12.hg19)
#norm <- minfi::preprocessRaw(minfiData::RGsetEx)
#data <- norm[,1]
#ctrl <- norm[,4]
#runConumee(data,ctrl,"segments")

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