shinyMethylSet-class {shinyMethyl} | R Documentation |
This class holds summarized data from Illumina methylation microarrays for interactive visualization purpose.
## 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"), array = new("character")) ## Data extraction / Accessors ## S4 method for signature 'shinyMethylSet' getMeth(object) ## S4 method for signature 'shinyMethylSet' getUnmeth(object) ## S4 method for signature 'shinyMethylSet' getBeta(object) ## S4 method for signature 'shinyMethylSet' getM(object) ## S4 method for signature 'shinyMethylSet' getCN(object) ## S4 method for signature 'shinyMethylSet' pData(object) ## S4 method for signature 'shinyMethylSet' sampleNames(object)
object |
A |
sampleNames |
A character vector |
phenotype |
A |
methQuantiles |
A list of 5 matrices containing several quantiles for the methylation values (between zero and infinity) separated by probe tpye and autosomal/sex probes. Each row is a quantile and each column is a sample. |
unmethQuantiles |
Similar to |
betaQuantiles |
Similar to |
mQuantiles |
Similar to |
cnQuantiles |
Similar to |
greenControls |
A list containing the matrices of different raw control probes intensities in the green channel |
redControls |
Similar to |
pca |
List containing the PCA scores for the 20,000 most variable CpGs and the percentages of variance explained |
originObject |
Name of the minfi object from which the data were extracted |
array |
Name of the Illumina array platform: 450k or EPIC |
These class is a representation of a 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
.
Instances are constructed using the shinyMethylSet
function with the
arguments outlined above.
In the following code, object
is a shinyMethylSet
.
getMeth(object)
, getUnmeth(object)
Get the Meth or Unmeth matrix.
getBeta(object)
get Beta, see details.
getM(object)
get M-values, see details.
getCN(object)
get copy number values which are defined as the sum of the methylation and unmethylation channel.
sampleNames(object)
Get the sampleNames
combine(object1,object2)
combine shinyMethylSet
objects
Jean-Philippe Fortin jfortin@jhsph.edu
Objects of this class are typically created by using the function
shinySummarize
on a RGChannelSet
or
GenomicRatioSet
.
showClass("shinyMethylSet")