# Function for performing Nearest Shrunken Centroid classification;
# it is a wrapper for the package 'pamr'.
# Arguments: two tables of frequencies for the training and the test sets,
# samples in rows, observations (features) in columns
perform.nsc = function(training.set,
test.set,
classes.training.set = NULL,
classes.test.set = NULL,
show.features = FALSE,
no.of.candidates = 3) {
# first, sanitizing the type of input data
if(length(dim(training.set)) != 2) {
stop("train set error: a 2-dimensional table (matrix) is required")
}
# if a vector (rather than a matrix) was used as a test set, a fake row
# will be added; actually, this will be a duplicate of the vector
if(is.vector(test.set) == TRUE) {
test.set = rbind(test.set, test.set)
rownames(test.set) = c("unknown", "unknown-copy")
# additionally, duplicating ID of the test classes (if specified)
if(length(classes.test.set) == 1) {
classes.test.set = c(classes.test.set, "unknown-copy")
}
}
# checking if the two sets are of the same size
if(length(test.set[1,]) != length(training.set[1,])) {
stop("training set and test set should have the same number of variables!")
}
# assigning classes, if not specified
if(length(classes.training.set) != length(rownames(training.set))) {
classes.training.set = c(gsub("_.*", "", rownames(training.set)))
}
if(length(classes.test.set) != length(rownames(test.set))) {
classes.test.set = c(gsub("_.*", "", rownames(test.set)))
}
#
# training_set and test_set preparation; adding class labels to both sets
classes = c(classes.training.set, classes.test.set)
input.data = as.data.frame(rbind(training.set,test.set))
training.classes = c(1:length(training.set[,1]))
mydata = list(x = t(input.data),
y = as.factor(classes),
geneid = as.character(1:length(colnames(training.set))),
genenames = colnames(training.set)
)
# training a model
model = pamr.train(mydata,sample.subset=c(1:length(classes.training.set)))
cat("\n")
# getting the discriminative features (if an appropriate option was chosen)
if(show.features == TRUE) {
the.features = pamr.listgenes(model,mydata,threshold=1,genenames=TRUE)#[,2]
} else {
the.features = NULL
}
# testing the model on "new" data (i.e. the test.set)
classification.results = pamr.predict(model,mydata$x,threshold=1, type="posterior")
selected.dist = classification.results[-c(1:length(training.set[,1])),]
if(no.of.candidates > length(unique(classes.training.set))) {
no.of.candidates = length(unique(classes.training.set))
}
# starting final variables
classification.results = c()
classification.scores = c()
classification.rankings = c()
for(h in 1:length(selected.dist[,1])) {
ranked.c = order(selected.dist[h,],decreasing=TRUE)[1:no.of.candidates]
current.sample = colnames(selected.dist)[ranked.c[1]]
classification.results = c(classification.results, current.sample)
#
current.ranking = colnames(selected.dist)[ranked.c]
current.scores = selected.dist[h,ranked.c]
classification.scores = rbind(classification.scores, current.scores)
classification.rankings = rbind(classification.rankings, current.ranking)
}
names(classification.results) = rownames(test.set)
rownames(classification.rankings) = rownames(test.set)
rownames(classification.scores) = rownames(test.set)
colnames(classification.rankings) = 1:no.of.candidates
colnames(classification.scores) = 1:no.of.candidates
# preparing a confusion table
predicted_classes = classification.results
expected_classes = classes.test.set
classes_all = sort(unique(as.character(c(expected_classes, classes.training.set))))
predicted = factor(as.character(predicted_classes), levels = classes_all)
expected = factor(as.character(expected_classes), levels = classes_all)
confusion_matrix = table(expected, predicted)
# shorten the names of the variables
y = classification.results
ranking = classification.rankings
scores = classification.scores
raw_scores = selected.dist
features = the.features
# predicted = predicted_classes
# expected = expected_classes
# misclassified = cv.misclassifications
attr(y, "description") = "classification results in a compact form"
# attr(misclassified, "description") = "misclassified samples [still not working properly]"
attr(predicted, "description") = "a vector of classes predicted by the classifier"
attr(expected, "description") = "ground truth, or a vector of expected classes"
attr(ranking, "description") = "predicted classes with their runner-ups"
attr(scores, "description") = "NSC decision scores, ordered according to candidates"
attr(raw_scores, "description") = "NSC decision scores in their original order"
attr(confusion_matrix, "description") = "confusion matrix for all cv folds"
results = list()
results$y = y
# results$misclassified = misclassified
results$predicted = predicted
results$expected = expected
results$ranking = ranking
results$scores = scores
results$raw_scores = raw_scores
results$confusion_matrix = confusion_matrix
# if 'features' is non-empty, add it as well:
if(is.null(features) == FALSE) {
attr(features, "description") = "the most distinctive features"
results$features = features
}
# adding some information about the current function call
# to the final list of results
results$call = match.call()
results$name = call("perform.nsc")
class(results) = "stylo.results"
return(results)
}
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