lpc (version 1.0.2.1)

PredictiveAdvantage: Plot predictive advantage of LPC vs. T

Description

This function plots the predictive advantage of LPC vs. T. The predictive advantage is the difference between the red and black curves. If the red curve is higher than the black curve on average, then LPC should be used instead of T on this data set.

Usage

PredictiveAdvantage(x,y,type,nreps=20,ngenes=100,
soft.thresh=NULL,censoring.status=NULL)

Arguments

x

The matrix of gene expression values; pxn where n is the number of observations and p is the number of genes.

y

A vector of length n, with an outcome for each observation. For two-class outcome, y's elements are 1 or 2. For quantitative outcome, y's elements are real-valued. For survival data, y indicates the survival time. For multiclass outcome, y is coded as 1,2,3,..

type

One of "regression" (for a quantitative outcome), "two class", "multiclass", or "survival".

nreps

Number of training/test set splits used in computing predictive advantage.

soft.thresh

Value of soft threshold used in L1 constraint for LPC. If NULL, then it will be computed adaptively.

ngenes

Number of genes to include in predictive advantage plot. (E.g., if ngenes=100 (default) then $E(|T_test| | |L_train|>alpha(L_train))$ and $E(|T_test| | |T_train|>alpha(T_train))$ will be plotted (see "Details"), where $alpha(L_train)$ and $alpha(T_train)$ are the 100th largest (in absolute value) T and LPC scores on the training set.)

censoring.status

For survival outcome only, a vector of length n which takes on values 0 or 1 depending on whether the observation is complete or censored.

Value

lpc

A vector of numGenes elements. The ith element is of the form $E(|T_test| | |L_train|>alpha(L_train))$, where $alpha(L_train)$ is the ith smallest (in absolute value) training set LPC score. Note that $L_train$ are LPC scores on the training set, $T_test$ are T scores on the test set.

t

A vector of numGenes elements. The ith element is of the form $E(|T_test| | |L_train|>alpha(T_train))$, where $alpha(T_train)$ is the ith smallest (in absolute value) training set T score, and where $T_train$ are T scores on the training set and $T_test$ are T scores on the test set.

Details

As explained in the paper, predictive advantage is computed by first splitting the data into a training set and a test set (each with 50% of the samples). Then, the following is computed: $E(|T_test| | |L_train|>alpha(L_train)) - E(|T_test| | |T_train|>alpha(T_train))$, where $T_test$ are the T scores on the test data, $T_train$ are the T scores on the training data, and $L_train$ are the LPC scores on the training data. $alpha(L_train)$ and $alpha(T_train)$ are the $alpha$ quantiles of the LPC and T scores on the training data. A large value of $E(|T_test| | |L_train|>alpha(L_train)) - E(|T_test| | |T_train|>alpha(T_train))$ suggests that LPC is superior to T on this data set.

References

Witten, D.M. and Tibshirani, R. (2008) Testing significance of features by lassoed principal components. Annals of Applied Statistics. http://www-stat.stanford.edu/~dwitten

Examples

# NOT RUN {
# Not run due to timing; uncomment to run

#set.seed(2)
#n <- 40 # 40 samples
#p <- 1000 # 1000 genes
#x <- matrix(rnorm(n*p), nrow=p) # make 40x1000 gene expression matrix
#y <-  rnorm(n) # quantitative outcome
## make first 50 genes differentially-expressed
#x[1:25,y<(-.5)] <- x[1:25,y<(-.5)]+ 1.5
#x[26:50,y<0] <- x[26:50,y<0] - 1.5
## compute LPC and T scores for each gene
#lpc.obj <- LPC(x,y, type="regression")
## Look at plot of Predictive Advantage
#pred.adv <-
#PredictiveAdvantage(x,y,type="regression",soft.thresh=lpc.obj$soft.thresh)
## Estimate FDRs for LPC and T scores
#fdr.lpc.out <-
#EstimateLPCFDR(x,y,type="regression",soft.thresh=lpc.obj$soft.thresh,nreps=50)
## Estimate FDRs for T scores only. This is quicker than computing FDRs
##    for LPC scores, and should be used when only T FDRs are needed. If we
##    started with the same random seed, then EstimateTFDR and EstimateLPCFDR
##    would give same T FDRs.
#fdr.t.out <- EstimateTFDR(x,y, type="regression")
## print out results of main function
#lpc.obj
## print out info about T FDRs
#fdr.t.out
## print out info about LPC FDRs
#fdr.lpc.out
## Compare FDRs for T and LPC on 6% of genes. In this example, LPC has
##    lower FDR.
#PlotFDRs(fdr.lpc.out,frac=.06)
## Print out names of 20 genes with highest LPC scores, along with their
##    LPC and T scores.
#PrintGeneList(lpc.obj,numGenes=20)
## Print out names of 20 genes with highest LPC scores, along with their
##    LPC and T scores and their FDRs for LPC and T.
#PrintGeneList(lpc.obj,numGenes=20,lpcfdr.out=fdr.lpc.out)




## Now, repeating everything that we did before, but using a
##   **survival** outcome

#set.seed(2)
#n <- 40 # 40 samples
#p <- 1000 # 1000 genes
#x <- matrix(rnorm(n*p), nrow=p) # make 40x1000 gene expression matrix
#y <-  rnorm(n) + 10 # survival times; must be positive
## censoring outcome: 0 or 1
#cens <- rep(1,40) # Assume all observations are complete
## make first 50 genes differentially-expressed
#x[1:25,y<9.5] <- x[1:25,y<9.5]+ 1.5
#x[26:50,y<10] <- x[26:50,y<10] - 1.5
#lpc.obj <- LPC(x,y, type="survival", censoring.status=cens)
## Look at plot of Predictive Advantage
#pred.adv <-
#PredictiveAdvantage(x,y,type="survival",soft.thresh=lpc.obj$soft.thresh,
#censoring.status=cens)
## Estimate FDRs for LPC scores and T scores
#fdr.lpc.out <- EstimateLPCFDR(x,y,type="survival",
#soft.thresh=lpc.obj$soft.thresh,nreps=20,censoring.status=cens)
## Estimate FDRs for T scores only. This is quicker than computing FDRs
##    for LPC scores, and should be used when only T FDRs are needed. If we
##    started with the same random seed, then EstimateTFDR and EstimateLPCFDR
##    would give same T FDRs.
#fdr.t.out <- EstimateTFDR(x,y, type="survival", censoring.status=cens)
## print out results of main function
#lpc.obj
## print out info about T FDRs
#fdr.t.out
## print out info about LPC FDRs
#fdr.lpc.out
## Compare FDRs for T and LPC scores on 10% of genes.
#PlotFDRs(fdr.lpc.out,frac=.1)
## Print out names of 20 genes with highest LPC scores, along with their
##    LPC and T scores.
#PrintGeneList(lpc.obj,numGenes=20)
## Print out names of 20 genes with highest LPC scores, along with their
##    LPC and T scores and their FDRs for LPC and T.
#PrintGeneList(lpc.obj,numGenes=20,lpcfdr.out=fdr.lpc.out)

 
# }