BSmooth.fstat {bsseq} | R Documentation

## 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 khansen@jhsph.edu

### 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
        }

[Package bsseq version 1.20.0 Index]