hapassoc: Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm
Version 1.2-8

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.

AuthorK. 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 publication2015-05-11 00:22:30
MaintainerK. Burkett <kburkett@uottawa.ca>
LicenseGPL-2
Version1.2-8
URL http://stat.sfu.ca/statgen/research/hapassoc.html
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("hapassoc")

Popular 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
See all...

All man pages Function index File listing

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

Functions

EMnull Source code
EMnullPHASE Source code
EMvar Source code
IPhi Source code
IPhiGamma Source code
IPhiGaussian Source code
RecodeHaplos Source code
SPhi Source code
SPhiGamma Source code
SPhiGaussian Source code
anova.hapassoc Man page Source code
codeHaploDM Source code
get.diplofreq Source code
getHaplos Source code
getPhenos Source code
handleMissings Source code
hapassoc Man page Source code
hypoDat Man page
hypoDatGeno Man page
isHetero Source code
isIn Source code
isMissing Source code
isMultiHetero Source code
logLik.hapassoc Man page Source code
loglikelihood Source code
makeHaploLab Source code
makeHaploLabN Source code
mlPhi Source code
mlPhiGamma Source code
momentPhiGamma Source code
onLoad Source code
onUnload Source code
pYgivenX Source code
pre.hapassoc Man page Source code
print.summary.hapassoc Source code
probY Source code
r.Omega Source code
summary.hapassoc Man page Source code

Files

inst
inst/CITATION
inst/ChangeLog
inst/doc
inst/doc/hapassoc.R
inst/doc/hapassoc.Rnw
inst/doc/hapassoc.pdf
src
src/getWts.c
src/tapply_sum.c
NAMESPACE
data
data/hypoDat.txt.gz
data/hypoDatGeno.txt.gz
R
R/hapassoc.R
R/RecodeHaplos.R
R/summaryHap.R
R/logLik_hapassoc.R
R/PreHap.R
R/zzz.R
vignettes
vignettes/hapassoc.Rnw
vignettes/burkett_biblio.bib
vignettes/jsslogo.jpg
MD5
build
build/vignette.rds
DESCRIPTION
man
man/hypoDat.Rd
man/summaryHap.Rd
man/anova_hapassoc.Rd
man/PreHap.Rd
man/hypoDatGeno.Rd
man/hapassoc.Rd
man/logLik_hapassoc.Rd
hapassoc documentation built on May 19, 2017, 7:57 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

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