discretizeExpressionValues {DFP}R Documentation

Function to discretize gene expression data

Description

Discretizes the gene expression data (float values) into ‘Low’, ‘Medium’ or ‘High’ labels.

Usage

discretizeExpressionValues(rmadataset, mfs, zeta = 0.5, overlapping = 2)

Arguments

rmadataset ExpressionSet with numeric values containing gene expression values (rows) of samples belonging to different categories (columns).
The ExpressionSet also contains an AnnotatedDataFrame with metadata regarding the classes to which each sample belongs.
mfs Membership functions to determine the discret value (linguistic label) corresponding to a given gene expression level.
zeta Threshold value which controls the activation of a linguistic label ('Low', 'Medium' or 'High').
The lower, the less posibilities of having genes with more than one assigned linguistic label.
Default value = 0.5. Range[0,1].
overlapping Modifies the number of membership functions used in the discretization process.
Possible values:
  1. ‘Low’, ‘Medium’, ‘High’.
  2. ‘Low’, ‘Low-Medium’, ‘Medium’, ‘Medium-High’, ‘High’.
  3. ‘Low’, ‘Low-Medium’, ‘Low-Medium-High’, ‘Medium’, ‘Medium-High’, ‘High’.
Default value = 2.

Value

Matrix containing discrete values according to the overlapping parameter after discretizing the gene expression values.
Includes an attribute types which determines the category of each sample.

Author(s)

Rodrigo Alvarez-Gonzalez
Daniel Glez-Pena
Fernando Diaz
Florentino Fdez-Riverola
Maintainer: Rodrigo Alvarez-Gonzalez <rodrigo.djv@uvigo.es>

References

F. Diaz; F. Fdez-Riverola; D. Glez-Pena; J.M. Corchado. Using Fuzzy Patterns for Gene Selection and Data Reduction on Microarray Data. 7th International Conference on Intelligent Data Engineering and Automated Learning: IDEAL 2006, (2006) pp. 1095-1102


[Package DFP version 1.0.0 Index]