prepareAxis {goCluster}R Documentation

Reduces a tree of selected items to a vector of non-overelapping regions with minimal p-value

Description

The function expects a tree representing clusters from a hierarchical clustering as input. Each cluster represented my contain only one selected annotation term per annotation. This is usually achieved by feeding the output of the minimizeSelection output to this function as input. prepareAxis will merge all overlapping clusters in the tree to the non-overlapping clusters with annotation terms of minimal p-values. This forms an axis along the genes originally used for clustering. When ordered according to the tree of the hierarchical clustering the vector can easily be used for display purposes.

Usage

prepareAxis(minSelection, Clusters, annotations)

Arguments

minSelection The tree of representing the clusters of the hierarchical tree. Each cluster may only contain zero or one selected annotation terms per annotation.
Clusters A tree of the same structure as given for minSelection but each node identifies the genes included in that cluster.
annotations The number of annotations represented by the tree.

Value

A list with a length that corresponds to the number of annotations present in the original tree. Each list item contains a vector that matches the list of genes. For each gene the annotation term with minimal p-values (if any) is given.

Author(s)

Gunnar Wrobel, work@gunnarwrobel.de, http://www.gunnarwrobel.de.

See Also

clusterVisualHclust-class

Examples

namedv1 <- c(0.01,0.1)
names(namedv1) <- c("GeneA", "GeneB")
namedv2 <- c(0.01,0.01)
names(namedv2) <- c("GeneB", "GeneC")
namedv3 <- c(0.5,0.1)
names(namedv3) <- c("GeneD", "GeneE")

a1 <- list(annotationA = namedv1,
           annotationB = namedv2,
           annotationC = namedv3)
a2 <- list(annotationA = namedv2,
           annotationB = namedv3,
           annotationC = namedv1)
b <- list(list(a1,a2),list(a2,a1))

c <- minimizeSelection(b, 3)

clusters <- list(list(c(1,2),c(8,9)),list(c(20,21),c(20,21)))

prepareAxis(c, clusters, 3)

[Package goCluster version 1.4.0 Index]