pamr.train {pamr}  R Documentation 
A function that computes a nearest shrunken centroid for gene expression (microarray) data
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)
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.class1/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 tstatistic, 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 classwise 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 
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.
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 
Trevor Hastie,Robert Tibshirani, Balasubramanian Narasimhan, and Gilbert Chu
Robert Tibshirani, Trevor Hastie, Balasubramanian Narasimhan, and Gilbert Chu Diagnosis of multiple cancer types by shrunken centroids of gene expression PNAS 99: 65676572. Available at www.pnas.org
#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)