Usage
# default method
as.methylumi (mn = NULL, un = NULL, bn = NULL, pv = NULL, qc = NULL, da = NULL,
fd = c("CHR", "DESIGN"), ad=NULL)
Arguments
mn
matrix of methylated signal intensities, each column representing a sample
(generic) or a MethyLumiSet, RGSet, or MethylSet object. Column names
are used to get Sentrix row and column by default, see '...'.
un
matrix of unmethylated signal intensities, each column representing a sample
(default method) or NULL when mn is an object containing methylated and
unmethylated values
bn
matrix of precalculated betas, each column representing a sample
pv
matrix of detection p-values, each column representing a sample
da
annotation data frame, such as x@featureData@data #methylumi package. If NULL (the default), the IlluminaHumanMethylation450kmanifest package is used. See the fd argument
qc
control probe intensities: list of 2 matrices, Cy3 and Cy5, with
rownames, such as produced by intensitiesByChannel(QCdata(x))
(methylumi package)
fd
vector of items of featureData, which by default is
just the chromosome and DESIGN (ie typeI or type II assay). Other
data can be included using the fd argument, available data
is listed by the function getColumns()