pvals function

Compute p-values for ridgeLinear and ridgeLogistic models

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).

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.

Returns

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.

References

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

Author(s)

Erika Cule

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)