Nothing
## ----loadLibraries, results = 'hide', echo = FALSE----------------------------
library(a4Classif)
library(ALL)
## ----loadData-----------------------------------------------------------------
data(ALL, package = "ALL")
ALL <- addGeneInfo(ALL)
ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
## ----lassoClassification------------------------------------------------------
resultLasso <- lassoClass(object = ALL, groups = "BTtype")
plot(resultLasso,
label = TRUE,
main = "Lasso coefficients in relation to degree of penalization."
)
topTable(resultLasso, n = 15)
## ----pamClassification--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
resultPam <- pamClass(object = ALL, groups = "BTtype")
plot(resultPam,
main = "Pam misclassification error versus number of genes."
)
topTable(resultPam, n = 15)
confusionMatrix(resultPam)
## ----randomForestClassification-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# 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-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ROCcurve(gene = "ABL1", object = ALL, groups = "BTtype")
## ----sessionInformation, echo = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
print(sessionInfo())
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