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=NULL, sample.subset=NULL,
         threshold = NULL, n.threshold = 30, 
        scale.sd = TRUE, threshold.scale = NULL, se.scale = NULL, offset.percent = 50,
         hetero=NULL, prior = NULL, remove.zeros = TRUE, sign.contrast="both",
ngroup.survival = 2)

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. Optional components- genenames, a vector of gene names, and geneid- a vector of gene identifiers.
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)
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.
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)
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 NULL, and prior is then taken to be n.class/n, where n is the overall sample size and n.class is the sample sizes in each class.
remove.zeros Remove threshold values yielding zero genes? Default TRUE
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''.
ngroup.survival Number of groups formed for survival data. Default 2

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 to pamr.train
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

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

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

# train classifier on all  data except class 4
results2 <- pamr.train(mydata,sample.subset=(mydata$y!=4))
 
# train classifier on  only the first 500 genes
results3 <- pamr.train(mydata,gene.subset=1:500)


[Package pamr version 1.28.0 Index]