get.fitted.leaf: Returs the leaf for each sample

In Pigengene: Infers biological signatures from gene expression data

Description

Taking as input a tree and data, this function determines the leaf each sample will fall in.

Usage

get.fitted.leaf(c5Tree, inpDTemp, epsi = 10^(-7))

Arguments

c5Tree	A decision tree of class C50 that uses module eigengenes, or NULL. If NULL, expression plots for all modules are created.
inpDTemp	The possibly new data matrix with samples on rows
epsi	A small perturbation to resolve the boundary issue

Value

A numeric vector of node indices named by samples (rows of inpDTemp)

Note

This function is tricky because C50 uses a global variable.

Author(s)

Amir Foroushani

See Also

Pigengene-package, make.decision.tree, compact.tree, compute.pigengene, module.heatmap, get.used.features, preds.at

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)
     f1 <- get.fitted.leaf(c5Tree=trees$c5Trees[["15"]], 
       inpDTemp=pigengene$eigengenes)

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