| BSmooth.fstat {bsseq} | R Documentation |
Compute F-statistics based on smoothed whole-genome bisulfite sequencing data.
BSmooth.fstat(BSseq, design, contrasts, verbose = TRUE)
BSseq |
An object of class |
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
|
verbose |
Should the function be verbose? |
TODO
An object of class BSseqStat.
Kasper Daniel Hansen khansen@jhsph.edu
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.
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
}