BayMethList-class: Class '"BayMethList"'
In Repitools: Epigenomic tools

Description Constructor Methods Author(s) See Also Examples

This S4 class captures the genomic windows together with the number of read counts obtained by affinity-enrichment sequencing experiments for a fully methylated control and one or more samples of interest. Furthermore CpG-density is stored.

Creates a BayMethList object:

BayMethList(windows, control, sampleInterest, cpgDens, f=matrix(), priorTab=list(), methEst=list(), maskEmpBayes=logical())

windows: A GRanges object.
control: A matrix of read counts obtained by an affinity enrichment sequencing experiment for the fully methylated (SssI) treated sample. The number of rows must be equal to length(windows). Each column contains the counts of one sample. The number of columns must be either one or equal to the number of columns of sampleInterest.
sampleInterest: A matrix of read counts obtained by an affinity enrichment sequencing experiment for the samples of interest. The number of rows must be equal to length(windows). Each column contains the counts of one sample.
cpgDens: A numeric vector containing the CpG density for windows. The length must be equal to length(windows)
fOffset: A matrix where each column contains the normalizing offsets for one sample. The number of rows must be either equal to one or the number of windows.
priorTab: A list containing for each sample of interest the prior parameters as determined by empBayes.
methEst: A list containing the methylation estimates as determined by methylEst.
maskEmpBayes: A logical vector indicating which bins should be masked out in the empirical Bayes analysis. TRUE indicates to neglect the bin in the empirical Bayes approach.

x[i]: signature(x = "BayMethList"): Creates a BayMethList object, keeping only the i entries.
length: signature(x= "BayMethList"): gets the number of genomic regions included.
control<-: signature(x = "BayMethList"): replace the control slot
control: signature(object = "BayMethList"): extract the control matrix slot.
cpgDens<-: signature(x = "BayMethList"): replace the cpgDens slot
cpgDens: signature(object = "BayMethList"): extract the cpgDens slot.
sampleInterest<-: signature(x = "BayMethList"): replace the sampleInterest slot
sampleInterest: signature(object = "BayMethList"): extract the sampleInterest matrix slot.
show: signature(object = "BayMethList"): show an overview of the object
windows<-: signature(x = "BayMethList"): replace the windows slot
windows: signature(object = "BayMethList"): extract the windows GRanges slot.
fOffset<-: signature(x = "BayMethList"): replace the fOffset slot
fOffset: signature(object = "BayMethList"): extract the fOffset slot.
priorTab<-: signature(x = "BayMethList"): replace the priorTab slot
priorTab: signature(object = "BayMethList"): extract the priorTab slot.
methEst<-: signature(x = "BayMethList"): replace the methEst slot
methEst: signature(object = "BayMethList"): extract the methEst slot.
maskEmpBayes<-: signature(x = "BayMethList"): replace the maskEmpBayes slot
maskEmpBayes: signature(object = "BayMethList"): extract the maskEmpBayes slot.
ncontrol: signature(object = "BayMethList"): get the number of provided SssI samples.
nsampleInterest: signature(object = "BayMethList"): get the number of provided samples of Interest.

Andrea Riebler and Mark Robinson

determineOffset, empBayes, methylEst

    if(require(BSgenome.Hsapiens.UCSC.hg18)){
        windows <- genomeBlocks(Hsapiens, chrs="chr21", width=100, spacing=100)
        cpgdens <- cpgDensityCalc(windows, organism=Hsapiens,  
            w.function="linear", window=700)  
        co <- matrix(rnbinom(length(windows), mu=10, size=2), ncol=1)
        sI <- matrix(rnbinom(2*length(windows), mu=5, size=2), ncol=2)
        bm <- BayMethList(windows=windows, control=co, sampleInterest=sI,
            cpgDens=cpgdens)

        cat("Number of genomic regions", length(bm), "\n")
        cat("Number of fully methylated control samples:", ncontrol(bm), "\n")
        cat("Number of samples of interest:", nsampleInterest(bm), "\n")
        bm[2:20]
    }