pvals {ridge}

Compute p-values for ridgeLinear and ridgeLogistic models

Description

Functions for computing, printing and plotting p-values for ridgeLinear and ridgeLogistic models. The p-values are computed using the significance test of Cule et al (2011).

Usage

pvals(x, ...)

## S3 method for class 'ridgeLinear'
pvals(x, ...)

## S3 method for class 'ridgeLogistic'
pvals(x, ...)

## S3 method for class 'pvalsRidgeLinear'
print(x, digits = max(3, getOption("digits") - 3),
signif.stars = getOption("show.signif.stars"), all.coef = FALSE, ...) 

## S3 method for class 'pvalsRidgeLogistic'
print(x, digits = max(3, getOption("digits") - 3),
signif.stars = getOption("show.signif.stars"), all.coef = FALSE, ...)

## S3 method for class 'pvalsRidgeLinear'
plot(x, y = NULL, ...)

## S3 method for class 'pvalsRidgeLogistic'
plot(x, y = NULL, ...)

Arguments

x

For the pvals methods, an object of class "ridgeLinear" or "ridgeLogistic", typically from a call to "linearRidge" or "logisticRidge". For the print and plot methods, an object of class "pvalsRidgeLinear" or "pvalsRidgeLogistic", typically from a call to "pvals".

digits

minimum number of significant digits to be used for most numbers

signif.stars

logical; if TRUE, P-values are additionally encoded visually as significance stars in order to help scanning of long coefficient tables. It defaults to the show.signif.stars slot of options.

all.coef

Logical. Should p-values for all the ridge regression parameters be printed, or only the one from the ridge parameter chosen using the method of Cule et al (2012)

y

Dummy argument for compatibility with the default plot method. Ignored.

...

further arguments to be passed to or from other methods

Details

Standard errors, test statistics and p-values are computed using coefficients and data on the scale that was used to fit them. If the coefficients were standardized before the model was fitted, then the p-values relate to the scaled data.

Value

For the pvals methods, an object of class "pvalsRidgeLinear" or "pvalsRidgeLogistic" which is a list with elements

coef

The (scaled) regression coefficients

se

The standard errors of the regression coefficients

tstat

The test statistic of the regression coefficients

pval

The p-values of the regression coefficients

isScaled

Were the data scaled before the regression coefficients were fitted?

For the print methods, the argument x is returned invisibly.

Author(s)

Erika Cule

References

Significance testing in ridge regression for genetic data. Cule, E. et al (2011) BMC Bioinformatics, 12:372

See Also

linearRidge, logisticRidge

Examples

data(GenBin)
mod <- logisticRidge(Phenotypes ~ ., data = as.data.frame(GenBin))
pvalsMod <- pvals(mod)
print(pvalsMod)
print(pvalsMod, all.coef = TRUE)
plot(pvalsMod)