summaryHap: Summarize results of the hapassoc function

In hapassoc: Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm

Summarize results of the hapassoc function

Description

Summary function for reporting the results of the hapassoc function in a similar style to the lm and glm summaries.

Usage

## S3 method for class 'hapassoc'
summary(object, ...)

Arguments

object	a list of class hapassoc output by the hapassoc function
...	additional arguments to the summary function (currently unused)

Details

See the hapassoc vignette, of the same name as the package, for details.

Value

call	The function call to hapassoc
subjects	The number of subjects used in the analysis
coefficients	Table of estimated coefficients, standard errors and Wald tests for each variable
frequencies	Table of estimated haplotype frequencies and standard errors
dispersion	Estimate of dispersion parameter (Moment estimator for gamma model)

References

Burkett K, McNeney B, Graham J (2004). A note on inference of trait associations with SNP haplotypes and other attributes in generalized linear models. Human Heredity, 57:200-206

Burkett K, Graham J and McNeney B (2006). hapassoc: Software for Likelihood Inference of Trait Associations with SNP Haplotypes and Other Attributes. Journal of Statistical Software, 16(2):1-19

See Also

pre.hapassoc,hapassoc.

Examples

data(hypoDat)
example.pre.hapassoc<-pre.hapassoc(hypoDat, 3)
example.regr <- hapassoc(affected ~ attr + h000+ h010 + h011 + h100 + pooled,
                     example.pre.hapassoc, family=binomial())

# Summarize the results:
summary(example.regr)

# Results:
#$coefficients
#               Estimate Std. Error      zscore   Pr(>|z|)
#(Intercept) -1.24114270  0.7820977 -1.58694079 0.11252606
#attr         0.74036920  0.2918205  2.53707057 0.01117844
#h000         1.14968352  0.5942542  1.93466627 0.05303126
#h010        -0.59318434  0.6569672 -0.90291311 0.36657201
#h011        -0.03615243  0.9161959 -0.03945928 0.96852422
#h100        -0.85329292  1.0203105 -0.83630709 0.40298217
#pooled       0.38516864  0.8784283  0.43847478 0.66104215
#
#$frequencies
#         Estimate Std. Error
#f.h000 0.26716394 0.03933158
#f.h001 0.25191674 0.03866739
#f.h010 0.21997138 0.03881578
#f.h011 0.10094795 0.02949617
#f.h100 0.09507014 0.02371878
#f.h101 0.02584918 0.01411881
#f.h110 0.01779455 0.01386080
#f.h111 0.02128613 0.01247265
#
#$dispersion
#[1] 1

hapassoc documentation built on May 28, 2022, 1:13 a.m.