IntClust (version 0.1.0)

PathwaysIter: Iterations of the pathway analysis

Description

The MLP method to perform pathway analysis is based on resampling of the data. Therefore it is recommended to perform the pathway analysis multiple times to observe how much the results are influenced by a different resample. The function PathwaysIter performs the pathway analysis as described in Pathways a specified number of times. The input can be one data set or a list as in Pathway.2 and Pathways.

Usage

PathwaysIter(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)

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 of the objects. The rows should correspond with the genes.

nrclusters

The number of clusters to cut the dendrogram in. 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 ("GOBP", "GOMF","GOCC", "KEGG" or "REACTOME"). Default is "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. 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: 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.

Value

This element is again a list with the following four elements:

objects

A list with the elements LeadCpds (the objects of interest) and OrderedCpds (all objects in the order of the clustering result)

Characteristics

The found (top) characteristics of the feauture data

Genes

A list with the elements TopDE (a table with information on the top genes) and AllDE (a table with information on all genes)

Pathways

A list with the element ranked.genesets.table which is a data frame containing the genesets, their p-values and their descriptions. The second element is nr.genesets and contains the used and total number of genesets.

Examples

# NOT RUN {
# }
# NOT RUN {
data(fingerprintMat)
data(targetMat)
data(geneMat)
data(GeneInfo)

MCF7_F = Cluster(fingerprintMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="flexible",gap=FALSE,maxK=55,StopRange=FALSE)
MCF7_T = Cluster(targetMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="flexible",gap=FALSE,maxK=55,StopRange=FALSE)

L=list(MCF7_F,MCF7_T)
names=c('FP','TP')

MCF7_Paths_FandT=PathwaysIter(List=L, geneExpr = geneMat, nrclusters = 7, method = 
c("limma", "MLP"), geneInfo = GeneInfo, geneSetSource = "GOBP", topP = NULL, 
topG = NULL, GENESET = NULL, sign = 0.05,niter=2,fusionsLog = TRUE, 
weightclust = TRUE, names =names)
# }