computeStat {bsseq} | R Documentation

## Compute a test statistic based on smoothed whole-genome bisulfite sequencing data.

### Description

Compute a test statistic based on smoothed whole-genome bisulfite sequencing data.

### Usage

        computeStat(BSseqStat, coef = NULL)

### Arguments

`BSseqStat` | An object of class `BSseqStat`, typically an object returned by `smoothSds(...)` and not constructed by the user.
`coef` | A vector indicating for which coefficients the statistic is to be computed (`coef = NULL` corresponds to testing all coefficients). If the length of the `coef` is 1 then the corresponding t-statistic is computed, otherwise the corresponding F-statistic is computed.

### Details

TODO

### Value

An object of class BSseqStat. More speciically, the input BSseqStat object with the computed statistics added to the `stats` slot (accessible with `getStats`).

### Author(s)

Kasper Daniel Hansen khansen@jhsph.edu

### See Also

`smoothSds` for the function to create the appropriate `BSseqStat` input object. `BSseqStat` also describes the return class. This function is likely to be followed by the use of `dmrFinder`.

### Examples

        if(require(bsseqData)) {
            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 <- smoothSds(BS.stat)
            BS.stat <- computeStat(BS.stat)
            BS.stat
        }

[Package bsseq version 1.18.0 Index]