BSmooth.fstat: Compute F-statistics based on smoothed whole-genome bisulfite...

In hansenlab/bsseq: Analyze, manage and store whole-genome methylation data

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

Description

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

Usage

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

Arguments

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?

Details

TODO

Value

An object of class BSseqStat.

Author(s)

Kasper Daniel Hansen [e-mail]

See Also

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.

Examples

    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
    }

hansenlab/bsseq documentation built on Nov. 6, 2024, 2:59 p.m.