scObject-class: Class "scObject" ~~~
Description
Objects of this class hold data used by the sciClone package,
including variant vaf data, copy number calls, clustering results,
density and purity calculations, etc.
Objects from the Class
Objects can be created by calls of the form new("scObject").Slots
vafs.merged:- Object of class
"data.frame"
a data frame containing variant positions, vafs, cn, clusters, etc
clust:- Object of class
"list"
a list containing the results of clustering the vafs
densities:- Object of class
"list"
list containing information on kernel density and peaks
dimensions:- Object of class
"numeric"
the number of dimensions that are being used for clustering
marginalClust:- Object of class
"list"
marginal clustering data
sampleNames:- Object of class
"character"
a vector of names corresponding to the input samples
vafs.1d:- Object of class
"list"
a list containing 1d vafs and clusters for each sample
ellipse.metadata:- Object of class
"list"
metadata related to confidence metric plotting
purities:- Object of class
"numeric"
list of estimated purities for each sample
Methods
No methods defined with class "scObject" in the signature.