bsseq (version 1.8.2)

BSmooth.fstat: 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?

Value

An object of class BSseqStat.

Details

TODO

See Also

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

Examples

  ## Not run: 
#     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
#     }
#   ## End(Not run)