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

Examples

Run this code

  ## 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)