carscore {care} | R Documentation |

`carscore`

estimates the vector of CAR scores, either using the standard
empirical estimator of the correlation matrix, or a shrinkage estimator.

carscore(Xtrain, Ytrain, lambda, diagonal=FALSE, verbose=TRUE)

`Xtrain` |
Matrix of predictors (columns correspond to variables). |

`Ytrain` |
Univariate response variable. |

`lambda` |
The correlation shrinkage intensity (range 0-1).
If not specified (the default) it is estimated using an
analytic formula from Sch\"afer and Strimmer (2005). For |

`diagonal` |
For |

`verbose` |
If |

The CAR scores are the correlations between the response and the Mahalanobis-decorrelated predictors. CAR score is an abbreviation for Correlation-Adjusted (marginal) coRelation, where the first correlation matrix refers dependencies among predictors.

In Zuber and Strimmer (2011) it is argued that squared CAR scores are a natural measure for variable importance and it is shown that variable selection based on CAR scores is highly efficient compared to competing approaches such as elastic net lasso, or boosting.

If the response is binary (or descrete) the corresponding quantity
are CAT scores (see `catscore`

).

`carscore`

returns
a vector containing the CAR scores (or marginal correlations for `diagonal=TRUE`

).

Verena Zuber and Korbinian Strimmer (http://strimmerlab.org).

Zuber, V., and K. Strimmer. 2011. High-dimensional regression and variable selection using CAR scores. Statist. Appl. Genet. Mol. Biol. 10: 34. <DOI:10.2202/1544-6115.1730>

# load care library library("care") ###### # empirical CAR scores for diabetes data data(efron2004) xnames = colnames(efron2004$x) n = dim(efron2004$x)[1] car = carscore(efron2004$x, efron2004$y, lambda=0) car # compare orderings # variables ordered by squared CAR scores xnames[order(car^2, decreasing=TRUE)] # "bmi" "s5" "bp" "s3" "s4" "s6" "sex" "age" "s2" "s1" # compare with ordering by t-scores / partial correlations pcor = pcor.shrink(cbind(efron2004$y,efron2004$x), lambda=0, verbose=FALSE)[-1,1] xnames[order(pcor^2, decreasing=TRUE)] # "bmi" "bp" "s5" "sex" "s1" "s2" "s4" "s6" "s3" "age" # compare with ordering by marginal correlations mcor = cor(efron2004$y,efron2004$x) #mcor = carscore(efron2004$x, efron2004$y, diagonal=TRUE, lambda=0) xnames[order(mcor^2, decreasing=TRUE)] # "bmi" "s5" "bp" "s4" "s3" "s6" "s1" "age" "s2" "sex" # decomposition of R^2 sum(car^2) slm(efron2004$x, efron2004$y, lambda=0, lambda.var=0)$R2 # pvalues for empirical CAR scores pval = 1-pbeta(car^2, shape1=1/2, shape2=(n-2)/2) pval <= 0.05 ###### # shrinkage CAR scores for Lu et al. (2004) data data(lu2004) dim(lu2004$x) # 30 403 # compute shrinkage car scores car = carscore(lu2004$x, lu2004$y) # most important genes order(car^2, decreasing=TRUE)[1:10] # compare with empirical marginal correlations mcor = cor(lu2004$y, lu2004$x) order(mcor^2, decreasing=TRUE)[1:10] # decomposition of R^2 sum(car^2) slm(lu2004$x, lu2004$y)$R2

[Package *care* version 1.1.10 Index]