minfi (version 1.18.4)

compartments: Estimates A/B compartments from Illumina methylation arrays

Description

Estimates A/B compartments as revealed by Hi-C by computing the first eigenvector on a binned probe correlation matrix.

Usage

compartments(object, resolution=100*1000, what = "OpenSea", chr="chr22", method = c("pearson", "spearman"), keep=TRUE)

Arguments

object

An object of class (Genomic)MethylSet or (Genomic)RatioSet

resolution

An integer specifying the binning resolution

what

Which subset of probes should be used?

chr

The chromosome to be analyzed.

method

Method of correlation.

keep

Should the correlation matrix be stored or not?

Value

GRanges containing the correlation matrix, the compartment eigenvector and the compartment labels (A or B) as metadata.

Details

This function extracts A/B compartments from Illumina methylation microarrays. Analysis of Hi-C data has shown that the genome can be divided into two compartments (A/B compartments) that are cell-type specific and are associated with open and closed chromatin respectively. The approximately 170,000 open sea probes on the 450k array can be used to estimate these compartments by computing the first eigenvector on a binned correlation matrix. The binning resolution can be specified by resolution, and by default is set to a 100 kb. We do not recommend higher resolutions because of the low-resolution probe design of the 450k array.

References

JP Fortin and KD Hansen. Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data. bioRxiv (2015). doi:10.1101/019000.

Examples

if (require(minfiData)) {
  GMset <- mapToGenome(MsetEx)
  comps <- compartments(GMset)
}