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

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.

Value

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

Author(s)

Jean-Philippe Fortin jfortin@jhsph.edu, Kasper D. Hansen kasperdanielhansen@gmail.com

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)
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(minfi)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: lattice
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/minfi/compartments.Rd_%03d_medium.png", width=480, height=480)
> ### Name: compartments
> ### Title: Estimates A/B compartments from Illumina methylation arrays
> ### Aliases: compartments createCorMatrix extractAB
> 
> ### ** Examples
> 
> if (require(minfiData)) {
+   GMset <- mapToGenome(MsetEx)
+   comps <- compartments(GMset)
+ }
Loading required package: minfiData
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>