integrative_model: Calculating integrative model

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

Description

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

Usage

integrative_model(methylation.matrix, methylation_model, expression.matrix, expression_model, house.keeping.genes)

Arguments

methylation.matrix	A DNA methylation matrix contains locus (in rows) and sample (in columns). The annotation of methylation locus was based on the hg38 reference genome.
methylation_model	The coeffecients of feature methylation locus.
expression.matrix	A gene expression matrix contains each gene (in rows) and sample (in columns). The expression matrix should be log-normalized.
expression_model	The coeffecients of feature genes.
house.keeping.genes	The house keeping genes used to normalized gene expression.

Examples

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.