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

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The following R functions are used for inference of trait associations with haplotypes and other covariates in generalized linear models. The functions are developed primarily for data collected in cohort or cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some SNPs.

Author
K. Burkett <kburkett@uottawa.ca>, B. McNeney <mcneney@sfu.ca>, J. Graham <jgraham@stat.sfu.ca>, with code for case-control data contributed by Zhijian Chen <z11chen@math.uwaterloo.ca>
Date of publication
2015-05-11 00:22:30
Maintainer
K. Burkett <kburkett@uottawa.ca>
License
GPL-2
Version
1.2-8
URLs

View on CRAN

Man pages

anova_hapassoc
Return likelihood ratio test of haplotype effect
hapassoc
EM algorithm to fit maximum likelihood estimates of trait...
hypoDat
Simulated data for a hypothetical binary trait
hypoDatGeno
Simulated data for a hypothetical genetic SNPs
logLik_hapassoc
Return log-likelihood
PreHap
Pre-process the data before fitting it with hapassoc
summaryHap
Summarize results of the hapassoc function

Files in this package

hapassoc
hapassoc/inst
hapassoc/inst/CITATION
hapassoc/inst/ChangeLog
hapassoc/inst/doc
hapassoc/inst/doc/hapassoc.R
hapassoc/inst/doc/hapassoc.Rnw
hapassoc/inst/doc/hapassoc.pdf
hapassoc/src
hapassoc/src/getWts.c
hapassoc/src/tapply_sum.c
hapassoc/NAMESPACE
hapassoc/data
hapassoc/data/hypoDat.txt.gz
hapassoc/data/hypoDatGeno.txt.gz
hapassoc/R
hapassoc/R/hapassoc.R
hapassoc/R/RecodeHaplos.R
hapassoc/R/summaryHap.R
hapassoc/R/logLik_hapassoc.R
hapassoc/R/PreHap.R
hapassoc/R/zzz.R
hapassoc/vignettes
hapassoc/vignettes/hapassoc.Rnw
hapassoc/vignettes/burkett_biblio.bib
hapassoc/vignettes/jsslogo.jpg
hapassoc/MD5
hapassoc/build
hapassoc/build/vignette.rds
hapassoc/DESCRIPTION
hapassoc/man
hapassoc/man/hypoDat.Rd
hapassoc/man/summaryHap.Rd
hapassoc/man/anova_hapassoc.Rd
hapassoc/man/PreHap.Rd
hapassoc/man/hypoDatGeno.Rd
hapassoc/man/hapassoc.Rd
hapassoc/man/logLik_hapassoc.Rd