palmer-package: PALMER (Constrained Biclustering Algorithm to Improve Pathway...

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

Description

This package provides functions for fitting palmer, a constrained biclustering approach that allows to identify indirect relationships among genes based on the text mining of biomedical literature, which allows researchers to utilize prior biological knowledge to guide identification of gene-gene associations.

Details

Package:	palmer
Type:	Package
Version:	0.1.0
Date:	2019-02-28
License:	GPL (>= 2)
LazyLoad:	yes

This package contains a main class, palmer, which represents PALMER model fit.

The main methods for the PALMER is palmer, which fits constrained biclustering.

Author(s)

Jin Hyun Nam

Maintainer: Dongjun Chung <[e-mail]>

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

library(palmer)

# Loading data

data(sdata)
data(pathway)

# Fit PALMER

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

# Extract Gene and GO term cluster and its probability

predict(fit.palmer)

# Visualize the clustering analysis result

plot(fit.palmer)

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