lpc (version 1.0.2.1)

LPC: Compute LPC score for each gene

Description

This is the main function for the Lassoed Principal Components (lpc) method. Given a matrix of gene expression data and a vector of outcome measurements (one per patient) and an outcome type, this function computes the LPC score for each gene. Simple scores are projected onto the eigenarrays (with an L1 constraint) in order to obtain LPC scores; these simple scores are Cox scores (for a survival outcome), two-sample t-statistics (for a two-class outcome) or standardized regression coefficients (for a regression/quantitative outcome).

Usage

LPC(x, y, type = "regression", soft.thresh = NULL, u =
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, and must be positive. For multiclass outcome, y must be coded as 1,2,3,...

type

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

soft.thresh

The value of the soft threshold to be used in the L1 regression of the scores onto the eigenarrays. If NULL, then it will be chosen adaptively.

u

The eigenarrays of the data matrix (useful if the data matrix is large, to avoid having to re-compute the SVD in order to run this function multiple times). If NULL, then the eigenarrays will be computed internally. Note that the eigenarrays have the same dimension as the data.

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

lpcscores

A vector of LPC scores, of length p (one for each gene).

tscores

A vector of T scores (Cox, two-sample t-stats, or standardized regression coefficients), of length p (one for each gene).

soft.thresh

The value of the soft threshold used.

coefs

The coefficients for the L1 regression of the scores onto the eigenarrays.

call

The call that was made to this function.

Details

Lassoed Principal Components (LPC) is a method for identifying features associated with an outcome, under the hypothesis that significant features occur in correlated sets. In particular, the method was designed for identifying genes in a microarray experiment that are associated with some outcome (e.g.: cancer vs. normal, survival time, tumor size). The method involves projecting simpler scores for each gene (e.g.: two-sample t-statistic, Cox score, standardized regression coefficients) onto the eigenarrays of the gene expression data matrix, subject to an L1 constraint. The fitted values are the LPC scores, which may result in a more accurate gene ranking than the initial simpler scores.

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 {
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=5)
# should run more reps in practice! Running just 5 in this example
# so that it runs fast.
# 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
### COMMENTED TO REDUCE RUN TIME -- 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) + 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=5,censoring.status=cens)
# Running just 5 reps so that things run quickly -- please run more in practice
## 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)


## Now, repeating everything that we did before, but using a
##   **multiclass** 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 <-  sample(1:4, n, rep=TRUE)
## make first 50 genes differentially-expressed
#x[1:50,y==1] <- x[1:50,y==1] + 1.5
#x[1:25,y==2] <- x[1:25,y==2] + 1
#x[1:50,y==3] <- x[1:50,y==3] - 1
#lpc.obj <- LPC(x,y, type="multiclass")
## Look at plot of Predictive Advantage
#pred.adv <-
#PredictiveAdvantage(x,y,type="multiclass",soft.thresh=lpc.obj$soft.thresh)
## Estimate FDRs for LPC scores and T scores
#fdr.lpc.out <-
#EstimateLPCFDR(x,y, type="multiclass",soft.thresh=lpc.obj$soft.thresh,
#nreps=20)
## 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="multiclass")
## 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)



# }