get.genes {Pigengene} | R Documentation

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

### 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)

[Package Pigengene version 1.16.0 Index]