PathwayAnalysis: Pathway analysis with intersection over iterations

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

Pathway analysis with intersection over iterations

Description

The PathwayAnalysis function performs pathway analysis multiple times via PathwaysIter and takes the intersection over the iterations via Geneset.intersect.

Usage

PathwayAnalysis(
  List,
  Selection = NULL,
  geneExpr = NULL,
  nrclusters = NULL,
  method = c("limma", "MLP"),
  geneInfo = NULL,
  geneSetSource = "GOBP",
  topP = NULL,
  topG = NULL,
  GENESET = NULL,
  sign = 0.05,
  niter = 10,
  fusionsLog = TRUE,
  weightclust = TRUE,
  names = NULL,
  seperatetables = FALSE,
  separatepvals = FALSE
)

Arguments

List	A list of clustering outputs or output of theDiffGenes function.
Selection	If pathway analysis should be conducted for a specific selection of objects, this selection can be provided here. Default is NULL.
geneExpr	The gene expression matrix or ExpressionSet of the objects.
nrclusters	Optional. The number of clusters to cut the dendrogram in. Default is NULL.
method	The methods for gene and pathway analysis. Default is c("limma","MLP").
geneInfo	A data frame with at least the columns ENTREZID and SYMBOL. Default is NULL.
geneSetSource	The source for the getGeneSets function, defaults to "GOBP".
topP	Overrules sign. The number of pathways to display for each cluster. Default is NULL.
topG	Overrules sign. The number of top genes to be returned. Default is NULL.
GENESET	Optional. Can provide own candidate gene sets. Default is NULL.
sign	The significance level to be handled. Default is 0.05.
niter	The number of times to perform pathway analysis. Default is 10.
fusionsLog	Logical. To be handed to ReorderToReference. Default is TRUE
weightclust	Logical. To be handed to ReorderToReference. Default is TRUE.
names	Optional. Names of the methods. Default is NULL.
seperatetables	Logical. Default is FALSE.
separatepvals	Logical. Default is FALSE.

Details

This function relies on the suggested Bioconductor packages 'MLP', 'biomaRt' and 'org.Hs.eg.db'.

Value

The intersection over the iterations of the pathway analysis.

Examples

## Not run: 
MCF7_PathsFandT=PathwayAnalysis(List=L, geneExpr = geneMat, nrclusters = 7,
method = c("limma","MLP"), geneInfo = GeneInfo, geneSetSource = "GOBP",niter=2)

## End(Not run)

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