README.md

In Liulab/impel: Integrative Model Predict recurrence of Early Lung cancer

impel

Integrative Methylation model to Predict recurrence of Early Lung cancer. A model constructed by DNA methylation of enhancer region, a model constructed by RNA expression of target genes, and a model integrating above two models. These three models could be used to predict the recurrence of early lung cancer.

Data Availability

The data analyzed in this study are available from the National Genomics Data Center (accession numbers: HRA000208).

install

library(devtools)
install_github("Liulab/impel")

Quick start

meth_model

The DNA methylationn model constructed by enhancer region to predict the recurrence of early lung cancer

data(methylation_matrix)
data(methylation_model)
res = meth_model(methylation.matrix=methylation_matrix,methylation_model=methylation_model)

exp_model

The expression model constructed by enhacer target to predict the recurrence of early lung cancer

data(expression.matrix)
data(expression_model)
data(house.keeping.genes)
res =  exp_model(expression.matrix=expression.matrix,expression_model=expression_model,house.keeping.genes=house.keeping.genes)

integrative_model

A model integrating DNA methylation of enhancer regionand RNA expression of target genes, to predict the recurrence of early lung cancer.

data(methylation_matrix)
data(methylation_model)
data(expression.matrix)
data(expression_model)
data(house.keeping.genes)
res =  integrative_model(methylation.matrix=methylation_matrix,methylation_model=methylation_model,
expression.matrix=expression.matrix,expression_model=expression_model,
house.keeping.genes=house.keeping.genes)

Liulab/impel documentation built on Dec. 17, 2021, 1:10 a.m.