RGSEA (version 1.6.2)

RGSEAfix: Random Gene Set Enrichment Analysis with fixed number of features

Description

This is the function for classification and feature selection with fixed number of features from top and bottom of the subtset features.

Usage

RGSEAfix(query, reference, queryclasses, refclasses, random = 5000, featurenum
 = 500, iteration = 100)

Arguments

query

A matrix, The query data. This is the data which the research wants to know the class.

reference

A matrix. The reference data. Based of the reference data, the research infer the class of query data.

queryclasses

A character vector. It contains the classes of query data. If you don't know the classes of query data, just give it a character vector equal to the number of query data.

refclasses

A character vector. It contains the classes of reference data. You must know it.

random

A numeric variable. The number of features in the subset randomly sampled from the whole features each time.

featurenum

A numeric varialbe. The number of features selected from top and bottom of the subset respectivelly.

iteration

A numeric varialbe. The times of random sampling.

Value

[1] The times of each sample in the reference dataset is the most similar to the query data. [2] The frequencey of features selected from the top and bottom of the subsets from the query data, if the query data is correcly classified.

Examples

if(interactive()) {
    data(e1)
    data(e2)
    RGSEAfix(e1,e2, queryclasses=colnames(e1), refclasses=colnames(e2),      
random=20000, featurenum=1000, iteration=100)->test
}