pamr.train {pamr} | R Documentation

## A function to train a nearest shrunken centroid classifier

### Description

A function that computes a nearest shrunken centroid for gene expression (microarray) data

### Usage

    pamr.train(data, gene.subset=1:nrow(data$x), sample.subset=1:ncol(data$x),
             threshold = NULL, n.threshold = 30,
            scale.sd = T, threshold.scale = NULL, se.scale = NULL, offset.percent = 50,
             hetero = NULL, prior = n.class/n, remove.zeros = T, sign.contrast="both")

### Arguments

`data` | The input data. A list with components: x- an expression genes in the rows, samples in the columns), and y- a vector of the class labels for each sample
`gene.subset` | Subset of genes to be used. Can be either a logical vector of length total number of genes, or a list of integers of the row numbers of the genes to be used
`sample.subset` |
`threshold` | A vector of threshold values for the centroid shrinkage. Default is a set of 30 values chosen by the software
`n.threshold` | Number of threshold values desired (default 30)
`hetero` | Should a heterogeneity transformation be done? If yes, hetero must be set to one of the class labels (see Details below). Default is no (hetero=NULL)
`scale.sd` | Scale each threshold by the wthin class standard deviations? Default: true
`threshold.scale` | Additional scaling factors to be applied to the thresholds. Vector of length equal to the number of classes. Default- a vectors of ones.
`se.scale` | Vector of scaling factors for the within class standard errors. Default is sqrt(1/n.class-1/n), where n is the overall sample size and n.class is the sample sizes in each class. This default adjusts for different class sizes.
`offset.percent` | Fudge factor added to the denominator of each t-statistic, expressed as a percentile of the gene standard deviation values. This is a small positive quantity to penalize genes with expression values near zero, which can result in very large ratios. This factor is expecially impotant for Affy data. Default is the median of the standard deviations of each gene.
`prior` | Vector of length the number of classes, representing prior probabilities for each of the classes. The prior is used in Bayes rule for making class prediction. Default is n.class/n, where n is the overall sample size and n.class is the sample sizes in each class.
`remove.zeros` | Whether to remove multiple solutions having zero genes
`sign.contrast` | Directions of allowed deviations of class-wise average gene expression from the overall average gene expression. Default is ``both'' (positive or negative). Can also be set to ``positive'' or ``negative''.

### Details

`pamr.train` fits a nearest shrunken centroid classifier to gene expression data. Details may be found in the PNAS paper referenced below. One feature not described there is "heterogeneity analysis". Suppose there are two classes labelled "A" and "B". CLass "A" is considered a normal class, and "B" an abnormal class. Setting hetero="A" transforms expression values x[i,j] to |x[i,j]- mean(x[i,j])| where the mean is taken only over samples in class "A". The transformed feature values are then used in Pam. This is useful when the abnormal class "B" is heterogeneous, i.e. a given gene might have higher expresion than normal for some class "B" samples, and lower for others. With more than 2 classes, each class is centered on the class specified by hetero.

### Value

A list with components

`y` | The outcome classes.
`yhat` | A matrix of predicted classes, each column representing the results from one threshold.
`prob` | A array of predicted class probabilities. of dimension n by nclass by n.threshold. n is the number samples, nclass is the number of classes, n.threshold is the number of thresholds tried
`centroids` | A matrix of (unshrunken) class centroids, n by nclass
`hetero` | Value of hetero used in call
`norm.cent` | Centroid of "normal group, if hetero was specified
`centroid.overall` |
`sd` | A vector of the standard deviations for each gene
`threshold` |
`nonzero` | A vector of the number of genes that survived the thresholding, for each threshold value tried
`threshold.scale` | A vector of threshold scale factors that were used
`se.scale` | A vector of standard error scale factors that were used
`call` | The calling sequence used
`prior` | The prior probabilities used
`errors` | The number of trainin errors for each threshold value

### Author(s)

Trevor Hastie,Robert Tibshirani, Balasubramanian Narasimhan, and Gilbert Chu

### References

Robert Tibshirani, Trevor Hastie, Balasubramanian Narasimhan, and Gilbert Chu Diagnosis of multiple cancer types by shrunken centroids of gene expression PNAS 99: 6567-6572. Available at www.pnas.org

### Examples

    set.seed(120)
    #generate some data
    x <- matrix(rnorm(1000*20),ncol=20)
    y <- sample(c(1:4),size=20,replace=TRUE)
    mydata <- list(x=x,y=factor(y))

    #run classifier
    results<-   pamr.train(mydata)

    # run classifier on all  data except class 4
    results2 <- pamr.train(mydata,sample.subset=(mydata$y!=4))

    # run classifier on  only the first 500 genes
    results3 <- pamr.train(mydata,gene.subset=1:500)

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