ClusterProbes: The ClusterProbes function

In gevaertlab/EpiMix: EpiMix: an integrative tool for the population-level analysis of DNA methylation

The ClusterProbes function

Description

This function uses the annotation for Illumina methylation arrays to map each probe to a gene. Then, for each gene, it clusters all its CpG sites using hierchical clustering and Pearson correlation as distance and complete linkage. If data for normal samples is provided, only overlapping probes between cancer and normal samples are used. Probes with SNPs are removed. This function is prepared to run in parallel if the user registers a parallel structure, otherwise it runs sequentially. This function also cleans up the sample names, converting them to the 12 digit format.

Usage

ClusterProbes(MET_data, ProbeAnnotation, CorThreshold = 0.4)

Arguments

MET_data	data matrix for methylation.
ProbeAnnotation	GRange object for probe annoation.
CorThreshold	correlation threshold for cutting the clusters.

Value

List with the clustered data sets and the mapping between probes and genes.

gevaertlab/EpiMix documentation built on July 20, 2023, 9:28 a.m.