BSmooth.fstat: Compute F-statistics based on smoothed whole-genome bisulfite...
In bsseq: Analyze, manage and store bisulfite sequencing data

Description Usage Arguments Details Value Author(s) See Also Examples

Compute F-statistics based on smoothed whole-genome bisulfite sequencing data.

1	BSmooth.fstat(BSseq, design, contrasts, verbose = TRUE)

`BSseq`	An object of class `BSseq`.
`design`	The design matrix of the bisulfite-sequencing experiment, with rows corresponding to arrays and columns to coefficients to be estimated.
`contrasts`	Numeric matrix with rows corresponding to columns in `design` and columns containing contrasts. May be a vector if there is only one contrast.
`verbose`	Should the function be verbose?

TODO

An object of class BSseqStat.

Kasper Daniel Hansen khansen@jhsph.edu

BSmooth for the input object and BSseq for its class. BSseqStat describes the return class. This function is likely to be followed by the use of smoothSds, computeStat, and dmrFinder.

    if(require(bsseqData)) {
    # limma required for makeContrasts()
    library(limma)
    data(keepLoci.ex)
    data(BS.cancer.ex.fit)
    BS.cancer.ex.fit <- updateObject(BS.cancer.ex.fit)
    ## Remember to subset the BSseq object, see vignette for explanation
    ## TODO: Kind of a forced example
    design <- model.matrix(~0 + BS.cancer.ex.fit$Type)
    colnames(design) <- gsub("BS\\.cancer\\.ex\\.fit\\$Type", "",
                             colnames(design))
    contrasts <- makeContrasts(
        cancer_vs_normal = cancer - normal,
        levels = design
    )
    BS.stat <- BSmooth.fstat(BS.cancer.ex.fit[keepLoci.ex,],
                             design,
                             contrasts)
    BS.stat

    #---------------------------------------------------------------------------
    # An example using a HDF5Array-backed BSseq object
    #
    library(HDF5Array)
    # See ?SummarizedExperiment::saveHDF5SummarizedExperiment for details
    hdf5_BS.cancer.ex.fit <- saveHDF5SummarizedExperiment(
        x = BS.cancer.ex.fit[keepLoci.ex, ],
        dir = tempfile())
    hdf5_BS.stat <- BSmooth.fstat(hdf5_BS.cancer.ex.fit,
                                  design,
                                  contrasts)
    hdf5_BS.stat
    }