get.genes {Pigengene} | R Documentation |
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.
get.genes(c5Tree = NULL, pigengene = NULL, queue = NULL, modules = NULL, pos=0, enhance = TRUE)
queue |
A character vector. The membership queue for a decsision tree. |
pos |
Number of genes that are considered from removal. Same interpretation as in
|
enhance |
If |
modules |
Named character vector listing the module assignments. |
c5Tree |
A decision tree of class |
pigengene |
An object in |
This function needs modules
and queue
, or alternatively,
c5Tree
and pigengene
.
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.
Pigengene-package
,
compact.tree
,preds.at
,
get.used.features
, make.decision.tree
## 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)