iterEquivClust: For each combination of the specified levels in the choosen...

In alexsanchezpla/goProfiles: goProfiles: an R package for the statistical analysis of functional profiles

Description

For each combination of the specified levels in the choosen GO ontologies, compute the equivalence threshold distance matrix and generate a dendrogram from it.

Usage

iterEquivClust(geneLists, ontos = c("BP", "MF", "CC"), ontoLevels = c(2, 3),
  trace = TRUE, onTheFlyDev = NULL, method = "complete",
  jobName = "Equivalence clustering",
  ylab = "Equivalence threshold distance", alpha = 0.05, precis = 0.001,
  ...)

Arguments

geneLists	list of character vectors, each vector stands for the gene names in a given gene set
ontos	character vector, (e.g. c("BP","MF")) indicating the GO ontologies to be analysed
ontoLevels	integer vector (e.g. 2:4) indicating the GO levels in these ontologies where the GO profiles are built
trace	boolean, the full process must be traced? Defaults to TRUE
onTheFlyDev	character, name of the graphical device where to immediately display the resulting diagrams. The appropriate names depend on the operating system. Defaults to NULL and then nothing is displayed. Otherwise, successive graphical windows are opened and the successive diagrams are displayed in them
method	character, one of the admissible methods in function hclust. Defaults to "complete"
jobName	character, main plot name, defaults to "Equivalence clustering"
ylab	character, label of the vertical axis of the plot, defaults to "Equivalence threshold distance"
alpha	simultaneous nominal significance level for the equivalence tests to be repeteadly performed, defaults to 0.05
precis	numerical precission in the iterative search of the equivalence threshold distances, defaults to 0.001
...	additional arguments to hclust

Value

An object of class iterEquivCluster. It is a list of length(ontos), one element for each ontology under study. Each element of this list is itself a list of length(ontoLevels) with elements of class equivClust, standing for the cluster equivalence analysis performed for each ontology and level analysed

Examples

## Not run: 
data(kidneyGeneLists)
kidneyGeneLists
genListsClusters <- iterEquivClust(kidneyGeneLists, ontoLevels = 2:3,
                                   jobName = "Kidney Gene Lists_Equivalence Clustering (complete)",
                                   ylab = "Equivalence threshold distance",
                                   orgPackage="org.Hs.eg.db", method = "complete")
genListsClusters[["BP"]][["Level 3"]]
class(genListsClusters[["BP"]][["Level 3"]])

## End(Not run)

alexsanchezpla/goProfiles documentation built on May 28, 2019, 4:54 p.m.