Basic class for storing DNA methylation and experimental quality information
Details
It is a virtual class and objects of type RnBSet should not be instantiated. Instead, the child classes are
used: RnBeadRawSet and RnBeadSet for Infinium HumanMethylation and
RnBiseqSet for bisulfite sequencing data
Slots
pheno
Sample annotations (phenotypic and processing data) in the form of a data.frame.
sites
A matrix object storing the identifiers of the methylation sites for which the
methylation information is present
meth.sites
matrix of methylation values. Every row corresponds to a methylation site,
and every column - to a sample.
covg.sites
matrix of coverage values. Every row corresponds to a methylation site,
and every column - to a sample.
regions
list of all identifiers of methylation sites for which methylation information
is available.
meth.regions
list of methylation matrix objects, one per available region type. Every row in a
matrix corresponds to a methylation site, and every column - to a sample.
covg.regions
list of coverage matrix objects, one per available region type.
Every row corresponds to a region, and every column - to a sample.
status
list with meta-information about the object.
assembly
character vector of length one, specifying the genome assembly which the object is linked to, e.g. "hg19".
target
character vector of length one, specifying the feature class:
"CpG" for sequencing data, "probes450" and "probes27" for
HumanMethylation450 and HumanMethylation27 microarrays respectively.
inferred.covariates
list with covariate information.
Can contain elements "sva" and "cell.types".
version
Package version in which the dataset was created.
Methods and Functions
pheno
Gets the phenotypic and processing data of the dataset.
samples
Gets the identifiers of all samples in the dataset.
summarized.regions
Gets the genomic annotations for
which methylation data is present.
meth
Gets a matrix of methylation values in the dataset.
mval
Gets a matrix of M values in the dataset.
covg
Gets the matrix of coverage values of the dataset.
remove.sites
Removes sites from the dataset.
remove.samples
Removes samples from the dataset.
addPheno,RnBSet-method
Add sample annotation to the dataset.
combine
Combines two datasets.
regionMapping,RnBSet-method
Retrieve the sites mapping to a given region type
rnb.sample.summary.table
Creates a sample summary table from an RnBSet object.
providing 
.