DFP (version 1.30.0)

readCSV: Creates an ExpressionSet with an AnnotatedDataFrame from CSV files

Description

This function creates an ExpressionSet with an AnnotatedDataFrame. To do this, it requires two CSV files in a predefined format:

1. ‘exprsData’ with the expression values of genes (in rows) of different samples (in columns).
2. ‘pData’ with the samples (in columns) and the metadata ‘class’ (the most important for the algorithm discriminantFuzzyPattern), ‘age’ and ‘sex’.

Usage

readCSV(fileExprs, filePhenodata)

Arguments

fileExprs

The path to the exprsData file.

filePhenodata

The path to the pData file.

Value

An ExpressionSet object with an AnnotatedDataFrame storing ‘class’, ‘age’ and ‘sex’ information.

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

Examples

dataDir <- system.file("extdata", package="DFP"); dataDir
fileExprs <- file.path(dataDir, "exprsData.csv"); fileExprs
filePhenodata <- file.path(dataDir, "pData.csv"); filePhenodata
rmadataset <- readCSV(fileExprs, filePhenodata); rmadataset
pData(phenoData(rmadataset))
exprs(rmadataset)[1:10,1:5]