BayMethList {Repitools} | R Documentation

## Class `"BayMethList"`

### Description

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.

### Constructor

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.

### Methods

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.

### Author(s)

Andrea Riebler and Mark Robinson

### See Also

determineOffset, empBayes, methylEst

### Examples

        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]
        }

[Package Repitools version 1.26.0 Index]