summary.snpBin {SimHap}R Documentation

Summarizing Single SNP analysis models

Description

Summary method for objects of class snpBin

Usage

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

Arguments

object object of class snpBin, the result of a call to snp.bin.
x an object of class summary.snpBin, the result of a call to
summary.snpBin.
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.snpBin returns an object of class summary.snpBin, a list with components

call the formula call.
terms terms attribute of the formula called in snp.bin.
df.residual the residual degrees of freedom.
df degrees of freedom parameter used in printing the model summary.
residuals as per glm. The working residuals, that is the residuals in the final iteration of the IWLS fit. Since cases with zero weights are omitted, their working residuals are NA.
coefficients summarized results from fitted model, including odds ratios, confidence intervals and p-values.
formula formula1 used in snp.bin.
LRT a likelihood ratio test, testing for significant improvement of the model when SNP parameters are included.
weights as per glm. The working weights, that is the weights in the final iteration of the IWLS fit.
AIC Akaike Information Criterion for the generalized linear model fit including SNPs.

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.bin, snp.quant

Examples


data(SNP.dat)

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

data(pheno.dat)
mymodel <- snp.bin(formula1=PLAQUE~AGE+SEX+SNP_1_add, 
        formula2=PLAQUE~AGE+SEX, geno=geno.dat, pheno=pheno.dat)
summary(mymodel)


[Package SimHap version 1.0.0 Index]