| readCSV {DFP} | R Documentation |
This function creates an ExpressionSet with an AnnotatedDataFrame. To do this, it requires two CSV files in a predefined format:
exprsData’ with the expression values of genes (in rows) of different samples (in columns).
pData’ with the samples (in columns) and the metadata ‘class’ (the most important for the algorithm discriminantFuzzyPattern), ‘age’ and ‘sex’.
readCSV(fileExprs, filePhenodata)
fileExprs |
The path to the exprsData file. |
filePhenodata |
The path to the pData file. |
An ExpressionSet object with an AnnotatedDataFrame storing ‘class’, ‘age’ and ‘sex’ information.
Rodrigo Alvarez-Gonzalez
Daniel Glez-Pena
Fernando Diaz
Florentino Fdez-Riverola
Maintainer: Rodrigo Alvarez-Gonzalez <rodrigo.djv@uvigo.es>
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
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]