Description Usage Arguments Details Value Author(s) References See Also Examples
compute the probability matrix of two or three or four categories classifiers with an option to define the specific model or user-defined model.
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y |
The multinomial response vector with two, three or four categories. It can be factor or integer-valued. |
d |
The set of candidate markers, including one or more columns. Can be a data frame or a matrix. |
method |
Specifies what method is used to construct the classifier based on the marker set in d. Available option includes the following methods:"multinom": Multinomial Logistic Regression which is the default method, requiring R package nnet;"tree": Classification Tree method, requiring R package rpart;"svm": Support Vector Machine (C-classification and radial basis as default), requiring R package e1071;"lda": Linear Discriminant Analysis, requiring R package lda. |
... |
Additional arguments in the chosen method's function. |
The function returns the probability matrix for predictive markers based on a user-chosen machine learning method. Currently available methods include logistic regression (default), tree, lda, svm and user-computed risk values.
The probability matrix of the classification using a particular learning method on a set of marker(s).
Ming Gao: gaoming@umich.edu
Jialiang Li: stalj@nus.edu.sg
Li, J. and Fine, J. P. (2008): ROC analysis with multiple tests and multiple classes: methodology and applications in microarray studies. Biostatistics. 9 (3): 566-576.
Li, J., Chow, Y., Wong, W.K., and Wong, T.Y. (2014). Sorting Multiple Classes in Multi-dimensional ROC Analysis: Parametric and Nonparametric Approaches. Biomarkers. 19(1): 1-8.
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