PathwaysSelection: Pathway analysis for a selection of objects

Description

Internal function of Pathways.

Usage

PathwaysSelection(List = NULL, Selection, geneExpr = NULL,
  nrclusters = NULL, method = c("limma", "MLP"), geneInfo = NULL,
  geneSetSource = "GOBP", topP = NULL, topG = NULL, GENESET = NULL,
  sign = 0.05, fusionsLog = TRUE, weightclust = TRUE, names = NULL)

Arguments

List

A list of clustering outputs or output of theDiffGenes function. The first element of the list will be used as the reference in ReorderToReference. The output of ChooseFeatures is also accepted.

Selection

If pathway analysis should be conducted for a specific selection of objects, this selection can be provided here. Selection can be of the type "character" (names of the objects) or "numeric" (the number of specific cluster). Default is NULL.

geneExpr

The gene expression matrix or ExpressionSet of the objects. The rows should correspond with the genes.

nrclusters

Optional. The number of clusters to cut the dendrogram in. The number of clusters should not be specified if the interest lies only in a specific selection of objects which is known by name. Otherwise, it is required. Default is NULL.

method

The method to applied to look for differentially expressed genes and related pathways. For now, only the limma method is available for gene analysis and the MLP method for pathway analysis. Default is c("limma","MLP").

geneInfo

A data frame with at least the columns ENTREZID and SYMBOL. This is necessary to connect the symbolic names of the genes with their EntrezID in the correct order. The order of the gene is here not in the order of the rownames of the gene expression matrix but in the order of their significance. 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. If not specified, only the significant genes are shown. Default is NULL.

topG

Overrules sign. The number of top genes to be returned in the result. If not specified, only the significant genes are shown. Defaults is NULL.

GENESET

Optional. Can provide own candidate gene sets. Default is NULL.

sign

The significance level to be handled. Default is 0.05.

fusionsLog

Logical. To be handed to ReorderToReference: indicator for the fusion of clusters. Default is TRUE

weightclust

Logical. To be handed to ReorderToReference: to be used for the outputs of CEC, WeightedClust or WeightedSimClust. If TRUE, only the result of the Clust element is considered. Default is TRUE.

names

Optional. Names of the methods. Default is NULL.