get.genes: List the (most relevant) genes for a decision tree.

In Pigengene: Infers biological signatures from gene expression data

Description

This function returns all genes that are left after shrinking (compacting ) a given tree. If enhance is set to TRUE, it makes sure that the output contains at least two genes from each used module.

Usage

get.genes(c5Tree = NULL, pigengene = NULL, queue = NULL, modules = NULL, pos=0,
  enhance = TRUE)

Arguments

queue	A character vector. The membership queue for a decsision tree.
pos	Number of genes that are considered from removal. Same interpretation as in preds.at
enhance	If enhance is set to TRUE, the function makes sure that the output contains at least two genes from each used module. Otherwise, exactly the pos first elements of the queue are removed from consideration.
modules	Named character vector listing the module assignments.
c5Tree	A decision tree of class C50.
pigengene	An object in pigengene-class, usually created by compute.pigengene.

Details

This function needs modules and queue, or alternatively, c5Tree and pigengene.

Value

A character vector containing the names of the genes involved in the modules whose eigengenes are used in the tree. If pos > 0, the first pos such genes with lowest absolute membership in their respective modules are filtered.

See Also

Pigengene-package, compact.tree,preds.at, get.used.features, make.decision.tree

Examples

     ## Data:
     data(aml)
     data(mds)
     data(pigengene)
     d1 <- rbind(aml,mds)

     ## Fiting the trees:
     trees <- make.decision.tree(pigengene=pigengene, Data=d1,
     saveDir="trees", minPerLeaf=15, doHeat=FALSE,verbose=3,
       toCompact=FALSE)
     g1 <- get.genes(c5Tree=trees$c5Trees[["15"]],pigengene=pigengene)

Pigengene documentation built on Nov. 8, 2020, 6:47 p.m.