MLInterfaces (version 1.48.0)

varImpStruct-class: Class "varImpStruct" -- collect data on variable importance from various machine learning methods

Description

collects data on variable importance

Arguments

Objects from the Class

Objects can be created by calls of the form new("varImpStruct", ...). These are matrices of importance measures with separate slots identifying algorithm generating the measures and variable names.

Slots

.Data:
Object of class "matrix" actual importance measures
method:
Object of class "character" tag
varnames:
Object of class "character" conformant vector of names of variables

Extends

Class "matrix", from data part. Class "structure", by class "matrix". Class "array", by class "matrix". Class "vector", by class "matrix", with explicit coerce. Class "vector", by class "matrix", with explicit coerce.

Methods

plot
signature(x = "varImpStruct"): make a bar plot, you can supply arguments plat and toktype which will use lookUp(...,plat,toktype) from the annotate package to translate probe names to, e.g., gene symbols.
show
signature(object = "varImpStruct"): simple abbreviated display
getVarImp
signature(object = "classifOutput", fixNames="logical"): extractor of variable importance structure; fixNames parameter is to remove leading X used to make variable names syntactic by randomForest (ca 1/2008). You can set fixNames to false if using hu6800 platform, because all featureNames are syntactic as given.
report
signature(object = "classifOutput", fixNames="logical"): extractor of variable importance data, with annotation; fixNames parameter is to remove leading X used to make variable names syntactic by randomForest (ca 1/2008). You can set fixNames to false if using hu6800 platform, because all featureNames are syntactic as given.

Examples

Run this code
library(golubEsets)
data(Golub_Merge)
library(hu6800.db)
smallG <- Golub_Merge[1001:1060,]
set.seed(1234)
opar=par(no.readonly=TRUE)
par(las=2, mar=c(10,11,5,5))
rf2 <- MLearn(ALL.AML~., smallG, randomForestI, 1:40, importance=TRUE,
 sampsize=table(smallG$ALL.AML[1:40]), mtry=sqrt(ncol(exprs(smallG))))
plot( getVarImp( rf2, FALSE ), n=10, plat="hu6800", toktype="SYMBOL")
par(opar)
report( getVarImp( rf2, FALSE ), n=10, plat="hu6800", toktype="SYMBOL")

Run the code above in your browser using DataCamp Workspace