PreparePathway: Prepare data for pathway analysis

In MosaiClusteR: An Umbrella Framework for Multi-Source and Multi-Omics Clustering

Prepare data for pathway analysis

Description

The PreparePathway function prepares the input for the pathway analysis by computing differentially expressed genes (via limma) for a selection of objects if these were not provided.

Usage

PreparePathway(Object, geneExpr, topG, sign)

Arguments

Object	A clustering output or DiffGenes output element.
geneExpr	The gene expression matrix or ExpressionSet of the objects.
topG	Overrules sign. The number of top genes. Default is NULL.
sign	The significance level to be handled. Default is 0.05.

Details

This function may rely on the suggested Bioconductor package 'limma'.

Value

A list with the p-values of the genes, the objects and the genes.

Examples

## Not run: 
PreparePathway(Object=MCF7_F,geneExpr=geneMat,topG=NULL,sign=0.05)

## End(Not run)

MosaiClusteR documentation built on Oct. 25, 2026, 1:08 a.m.