pamr.decorrelate {pamr}

A function to decorrelate (adjust) the feature matrix with respect to some additional predictors

Description

A function to decorrelate (adjust) the feature matrix with respect to some additional predictors

Usage

pamr.decorrelate(
  x,
  adjusting.predictors,
  xtest = NULL,
  adjusting.predictors.test = NULL
)

Arguments

x

Matrix of training set feature values, with genes in the rows, samples in the columns

adjusting.predictors

List of training set predictors to be used for adjustment

xtest

Optional matrix of test set feature values, to be adjusted in the same way as the training set

adjusting.predictors.test

Optional list of test set predictors to be used for adjustment

Details

pamr.decorrelate Does a least squares regression of each row of x on the adjusting predictors, and returns the residuals. If xtest is provided, it also returns the adjusted version of xtest, using the training set least squares regression model for adjustment

Value

A list with components

x.adj

Adjusted x matrix

xtest.adj

Adjusted xtest matrix, if xtest we provided

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
suppressWarnings(RNGversion("3.5.0"))
set.seed(120)

x<-matrix(rnorm(1000*20),ncol=20)
y<-c(rep(1,10),rep(2,10))
adjusting.predictors=list(pred1=rnorm(20), pred2=as.factor(sample(c(1,2),replace
=TRUE,size=20)))
xtest=matrix(rnorm(1000*10),ncol=10)
adjusting.predictors.test=list(pred1=rnorm(10), pred2=as.factor(sample(c(1,2),replace
=TRUE,size=10)))

# decorrelate training x wrt adjusting predictors

x.adj=pamr.decorrelate(x,adjusting.predictors)$x.adj
# train classifier with adjusted x

d=list(x=x.adj,y=y)
a<-pamr.train(d)

# decorrelate training and test x wrt adjusting predictors, then make
#predictions for test set

temp <- pamr.decorrelate(x,adjusting.predictors, xtest=xtest,
                         adjusting.predictors.test=adjusting.predictors.test)

d=list(x=temp$x.adj,y=y)
a<-pamr.train(d)
aa<-pamr.predict(a,temp$xtest.adj, threshold=.5)