summary.snpQuant {SimHap}R Documentation

Summarizing single SNP analysis models for quantitative outcomes

Description

Summary method for objects of class snpQuant

Usage

## S3 method for class 'snpQuant':
summary(object, ...)
## S3 method for class 'summary.snpQuant':
print(x, digits = max(3, getOption("digits") - 3), 
        signif.stars = getOption("show.signif.stars"), ...)

Arguments

object an object of class snpQuant, a result of a call to snp.quant.
x an object of class summary.snpQuant, the result of a call to
summary.snpQuant.
digits the number of significant digits to use when printing.
signif.stars logical. If TRUE, ``significance stars" are printed for each coefficient.
... further arguments passed to or from other methods.

Value

summary.snpQuant returns an object of class summary.snpQuant, a list with components

call the formula call.
terms terms attribute of the formula called in snp.quant.
residuals the residuals, that is response minus fitted values.
df.residuals the residual degrees of freedom.
na.action method used for missing data.
df residual degrees of freedom.
sigma residual standard error.
coefficients summarized results from fitted model, including coefficients, standard errors and p-values.
formula formula1 used in snp.quant.
LRT likelihood ratio test comparing the model with SNP variables compared to the model without SNPs.
AIC Akaike information criterion for the full fitted model.
rsquared adjusted r-squared values for the fitted model.
predicted.values estimated marginal means for a chosen model term.

Author(s)

Pamela A. McCaskie

References

McCaskie, P.A., Carter, K.W. Hazelton, M., Palmer, L.J. (2007) SimHap: A comprehensive modeling framework for epidemiological outcomes and a multiple-imputation approach to haplotypic analysis of population-based data, [online] www.genepi.org.au/simhap.

See Also

snp.quant, snp.bin

Examples


data(SNP.dat)

# convert SNP.dat to format required by snp.quant
geno.dat <- SNP2Geno(SNP.dat, baseline=c("MM", "11", "GG", "CC"))

data(pheno.dat)
mymodel <- snp.quant(formula1=HDL~AGE+SBP+factor(SNP_1_add),
        formula2=HDL~AGE+SBP, geno=geno.dat, pheno=pheno.dat)
summary(mymodel)


[Package SimHap version 1.0.0 Index]