palmer-class: Class "palmer"

In dongjunchung/palmer: PALMER: A Constrained Biclustering Algorithm to Improve Pathway Annotation Based on the Biomedical Literature Mining

Description

This class represents palmer fit.

Objects from the Class

Objects can be created by calls of the form new("palmer", ...).

Slots

data

Object of class "matrix", representing the raw data for PALMER model.

init

Object of class "list", representing the setting for PALMER model fitting.

result

Object of class "list", representing the fitted PALMER model.

Methods

show

signature(object = "palmer"): provide brief summary of the object.

predict

signature(object = "palmer"): provide Gene and GO term cluster and its probability.

plot

signature(x = "palmer", y=missing): provide visualization of constrained biclustersing analysis result.

Author(s)

Jin Hyun Nam

References

Nam JH, Couch D, Silveira W.A, Yu Z and Chung D (2019) ”PALMER: A constrained biclustering Algorithm to improve pathway annotation based on the biomedical literature mining”.

See Also

palmer.

Examples

showClass("palmer")

data(sdata)
data(pathway)

fit.palmer <- palmer(X=sdata,path=pathway,K=2,L=3,B=100)
fit.palmer
predict(fit.palmer)
plot(fit.palmer)

dongjunchung/palmer documentation built on Aug. 4, 2020, 5:16 p.m.