## Constructor
shinyMethylSet(sampleNames = new("character"),
phenotype = new("data.frame"),
mQuantiles = new(vector("list",5)),
betaQuantiles = new(vector("list",5)),
methQuantiles = new(vector("list",5)),
unmethQuantiles = new(vector("list",5)),
cnQuantiles = new(vector("list",5)),
greenControls = new(vector("list",12)),
redControls = new(vector("list",12)),
pca = new("list"),
originObject = new("character"))
## Data extraction / Accessors
## S3 method for class 'shinyMethylSet':
getMeth(object)
## S3 method for class 'shinyMethylSet':
getUnmeth(object)
## S3 method for class 'shinyMethylSet':
getBeta(object)
## S3 method for class 'shinyMethylSet':
getM(object)
## S3 method for class 'shinyMethylSet':
getCN(object)
## S3 method for class 'shinyMethylSet':
pData(object)
## S3 method for class 'shinyMethylSet':
sampleNames(object)
shinyMethylSet
.data.frame
object.Meth
Meth
but for Beta-valuesMeth
but for M-valuesMeth
but for Copy NumbergreenControls
but for the red channelshinyMethylSet
function with the
arguments outlined above.Meth
matrix and a
Unmeth
matrix linked to a pData
data frame. A creationMethod slot is present to indicate from which object type
the shinyMethylSet
has been created: either a
RGChannelSet
or GenomicRatioSet
A MethylSet
stores meth
and Unmeth
.
shinySummarize
on a RGChannelSet
or
GenomicRatioSet
.