OmicsMarkeR (version 1.4.2)

feature.table: Feature Consistency Table

Description

Extracts and sorts the features identified for a given method.

Usage

feature.table(features, method)

Arguments

features

A fs.stability fitted object

method

Algorithm of interest Available options are "plsda" (Partial Least Squares Discriminant Analysis), "rf" (Random Forest), "gbm" (Gradient Boosting Machine), "svm" (Support Vector Machines), "glmnet" (Elastic-net Generalized Linear Model), and "pam" (Prediction Analysis of Microarrays)

Value

A data frame containing:

features

Features identified by model

consistency

Number of iterations feature was identified

frequency

Frequency of iterations the feature was identified

Examples

dat.discr <- create.discr.matrix(
    create.corr.matrix(
        create.random.matrix(nvar = 50, 
                             nsamp = 100, 
                             st.dev = 1, 
                             perturb = 0.2)),
    D = 10
)

vars <- dat.discr$discr.mat
groups <- dat.discr$classes

fits <- fs.stability(vars, 
                     groups, 
                     method = c("plsda", "rf"), 
                     f = 10, 
                     k = 3, 
                     k.folds = 10, 
                     verbose = 'none')

feature.table(fits, "plsda")