IntClust (version 0.1.0)

ChooseCluster: Interactive plot to determine DE Genes and DE features for a specific cluster

Description

If desired, the function produced a dendrogram of a clustering results. One or multiple cluster can be indicated by a mouse click. From these clusters DE genes and characteristic features are determined. It is also possible to provide the objects of interest without producing the plot. Note, it is required to click on the dendrogram branches, not on the objects. #' @export ChooseCluster

Usage

ChooseCluster(Interactive = TRUE, leadCpds = NULL, clusterResult = NULL,
  colorLab = NULL, binData = NULL, contData = NULL, datanames = c("FP"),
  geneExpr = NULL, topChar = 20, topG = 20, sign = 0.05,
  nrclusters = NULL, cols = NULL, n = 1)

Arguments

Interactive

Logical. Whether an interactive plot should be made. Defaults to TRUE.

leadCpds

A list of the objects of the clusters of interest. If Interactive=TRUE, these are determined by the mouse-click and it defaults to NULL.

clusterResult

The output of one of the aggregated cluster functions, The clustering result of interest. Default is NULL.

colorLab

The clustering result the dendrogram should be colored after as in ClusterPlot. It is the output of one of the clustering functions.

binData

A list of the binary feature data matrices. These will be evaluated with the fisher's extact test. Default is NULL.

contData

A list of continuous data sets of the objects. These will be evaluated with the t-test. Default is NULL.

datanames

A vector with the names of the data matrices. Default is NULL.

geneExpr

A gene expression matrix, may also be an ExpressionSet. The rows should correspond with the genes. Default is NULL.

topChar

The number of top characteristics to return. If NULL, only the significant characteristics are saved. Default is NULL.

topG

The number of top genes to return. If NULL, only the significant genes are saved. Default is NULL.

sign

The significance level. Default is 0.05.

nrclusters

Optional. The number of clusters to cut the dendrogram in. If NULL, the dendrogram will be plotted without colors to discern the different clusters. Default is NULL.

cols

The colors to use in the dendrogram. Default is NULL.

n

The number of clusters one wants to identify by a mouse click. Default is 1.

Value

The returned value is a list with one element per cluster of interest indicated by the prefix "Choice". This element is again a list with the following three 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 feature 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)

Details

The DE genes are determined by testing for significance of the specified cluster versus all other objects combined. This is performed by the limma function. The binary features are evaluated with the fisher exact test while the continuous features are tested with the t-test. Multiplicity correction is included.

Examples

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

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)

MCF7_Interactive=ChooseCluster(Interactive=TRUE,leadCpds=NULL,clusterResult=MCF7_T,
colorLab=MCF7_F,binData=list(fingerprintMat),datanames=c("FP"),geneExpr=geneMat,
topChar = 20, topG = 20,nrclusters=7,n=1)
# }