lociLikelihoods {segmentSeq} | R Documentation

## Evaluates the posterior likelihoods of each region defined by a segmentation map as a locus.

### Description

An empirical Bayesian approach that takes a segmentation map and uses this to bootstrap posterior likelihoods on each region being a locus for each replicate group.

### Usage

    lociLikelihoods(cD, aD, newCounts = FALSE, bootStraps = 3,
                    inferNulls = TRUE, nasZero = FALSE, usePosteriors =
    TRUE, tail = 0.1, subset = NULL, cl)

### Arguments

`cD` | A `lociData` object that defines a segmentation map.
`aD` | An `alignmentData` object.
`newCounts` | Should new counts be evaluated for the segmentation map in ‘cD’ before calculating loci likelihoods? Defaults to FALSE
`bootStraps` | What level of bootstrapping should be carried out on the inference of posterior likelihoods? See the baySeq function `getLikelihoods.NB` for a discussion of bootstrapping.
`inferNulls` | Should null regions be inferred from the gaps between segments defined by the ‘cD’ object?
`nasZero` | If FALSE, any locus with a posterior likelihood ‘NA’ in the existing segmentation map is treated as a null region for the first bootstrap; If TRUE, it is ignored for the first bootstrap.
`usePosteriors` | If TRUE, the function uses the existing likelihoods to weight the prior estimation of parameters. Defaults to TRUE.
`tail` | The cutoff for the tail of the distribution to be used in pre-calculating data for methylation analysis. See `methObservables`.
`subset` | A subset of the data on which to calculate the likelihoods.
`cl` | A SNOW cluster object, or NULL. See Details.

### Details

A `'cluster'` object (package: snow) may be used for parallelisation of this function when examining large data sets. Passing NULL to this variable will cause the function to run in non-parallel mode.

### Value

A `lociData` object.

### Author(s)

Thomas J. Hardcastle

### Examples

    # Define the files containing sample information.

    datadir <- system.file("extdata", package = "segmentSeq")
    libfiles <- c("SL9.txt", "SL10.txt", "SL26.txt", "SL32.txt")

    # Establish the library names and replicate structure.

    libnames <- c("SL9", "SL10", "SL26", "SL32")
    replicates <- c(1,1,2,2)

    # Process the files to produce an `alignmentData' object.

    alignData <- readGeneric(file = libfiles, dir = datadir, replicates =
    replicates, libnames = libnames, gap = 100)

    # Process the alignmentData object to produce a `segData' object.

    sD <- processAD(alignData, gap = 100, cl = NULL)

    # Use the segData object to produce a segmentation of the genome, but
    # without evaluating posterior likelihoods.

    segD <- heuristicSeg(sD = sD, aD = alignData,
        subRegion = data.frame(chr= ">Chr1", start = 1, end = 1e5),
        getLikes = FALSE, cl = NULL)

    # Use the lociData function to evaluate the posterior likelihoods directly.

    lociData <- lociLikelihoods(segD, aD = alignData, bootStraps = 5,
    inferNulls = TRUE, cl = NULL)

[Package segmentSeq version 2.28.0 Index]