GEcollection-class: Class "GEcollection"
In methylPipe: Base resolution DNA methylation data analysis

Description Objects from the Class Methods Author(s) Examples

This class is used in the methylPipe library to define and manipulate a set of genomic regions and the associated DNA methylation patterns

This class is an extension of the RangedSummarizedExperiment class from the SummarizedExperiment package. Objects can be created using the function profileDNAmetBin which determines the absolute and relative methylation level by filling the binC, binmC and binrC slots. The assays slot of the RangedSummarizedExperiment class here consists of four matrices:

binC: each genomic region is divided in one or more bins and for each bin the density (per bp) of potential methylation sites is determined.
binmC: each genomic region is divided in one or more bins and for each bin the density (per bp) of methylation events is determined.
binrC: each genomic region is divided in one or more bins and for each bin the relative mC/C content is determined.
binscore: each genomic region is divided in one or more bins and scores can be assigned to them. In particular, it can be convenient for storing reads count for each bin of each genomic region.

The minimal set of data to create a GEcollection object is a set of genomic regions to be provided as a GRanges object and a dataset of class BSdata.

chr: signature(object = "GEcollection"): extracts the chr assignment of the genomic regions
Strand: signature(object = "GEcollection"): extracts the strand assignment of the genomic regions
binC: signature(object = "GEcollection"): extracts the binC matrix
binmC: signature(object = "GEcollection"): extracts the binmC matrix
binrC: signature(object = "GEcollection"): extracts the binrC matrix
binscore: signature(object = "GEcollection"): extracts the binscore matrix
binscore<-: signature(object = "GEcollection"): replaces the binscore matrix
nbins: signature(object = "GEcollection"): returns the number of bins

Kamal Kishore

require(BSgenome.Hsapiens.UCSC.hg18)
uncov_GR <- GRanges(Rle('chr20'), IRanges(c(14350,69251,84185), c(18349,73250,88184)))
H1data <- system.file('extdata', 'H1_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
H1.db <- BSdata(file=H1data, uncov=uncov_GR, org=Hsapiens)
gr_file <- system.file('extdata', 'GR_chr20.Rdata', package='methylPipe')
load(gr_file)
gec.H1 <- profileDNAmetBin(GenoRanges=GR_chr20, Sample=H1.db, mcCLASS='mCG')
gec.H1