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This document explains the functionalities available in the a4Classif package.
This package contains for classification of Affymetrix microarray data,
stored in an ExpressionSet
.
This package integrates within the Automated Affymetrix Array Analysis
suite of packages.
library(a4Classif) library(ALL)
To demonstrate the functionalities of the package, the ALL
dataset is used.
The genes are annotated thanks to the addGeneInfo
utility function
of the a4Preproc
package.
data(ALL, package = "ALL") ALL <- addGeneInfo(ALL) ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
resultLasso <- lassoClass(object = ALL, groups = "BTtype") plot(resultLasso, label = TRUE, main = "Lasso coefficients in relation to degree of penalization." ) topTable(resultLasso, n = 15)
resultPam <- pamClass(object = ALL, groups = "BTtype") plot(resultPam, main = "Pam misclassification error versus number of genes." ) topTable(resultPam, n = 15) confusionMatrix(resultPam)
# select only a subset of the data for computation time reason ALLSubset <- ALL[sample.int(n = nrow(ALL), size = 100, replace = TRUE), ] resultRf <- rfClass(object = ALLSubset, groups = "BTtype") plot(resultRf) topTable(resultRf, n = 15)
ROCcurve(gene = "ABL1", object = ALL, groups = "BTtype")
print(sessionInfo())
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