haplo.stats: Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
Version 1.7.7

Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.

Browse man pages Browse package API and functions Browse package files

AuthorSinnwell JP, Schaid DJ
Date of publication2016-04-06 01:10:36
MaintainerJason P. Sinnwell <sinnwell.jason@mayo.edu>
LicenseGPL (>= 2)
Version1.7.7
URL http://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("haplo.stats")

Man pages

anova.haplo.glm: Analysis of variance for haplo.glm model fit
chisq.power: Power and sample size for the chi-square distribution
find.haplo.beta.qt: Find beta coefficients for risk haplotypes, for specified r2
fitted.haplo.glm: Fitted values from haplo.glm fit
f.power: Power and sample size for the F distribution
geno1to2: convert genotype matrix from 1-column 2-column
geno.count.pairs: Counts of Total Haplotype Pairs Produced by Genotypes
get.hapPair: Get a list of objects for haplotype pairs
Ginv: Compute Generalized Inverse of Input Matrix
haplo.cc: Haplotype Association Analysis in a Case-Control design
haplo.design: Build a design matrix for haplotypes
haplo.em: EM Computation of Haplotype Probabilities, with Progressive...
haplo.em.control: Create the Control Parameters for the EM Computation of...
haplo.em.fitter: Compute engine for haplotype EM algorithm
haplo.glm: GLM Regression of Trait on Ambiguous Haplotypes
haplo.glm.control: Create list of control parameters for haplo.glm
haplo.group: Frequencies for Haplotypes by Grouping Variable
haplo.hash: Integer Rank Codes for Haplotypes
haplo.model.frame: Sets up a model frame for haplo.glm
haplo.power.cc: Compute either power or sample size for haplotype...
haplo.power.qt: Compute either power or sample size for haplotype...
haplo.scan: Search for a trait-locus by sliding a fixed-width window over...
haplo.score: Score Statistics for Association of Traits with Haplotypes
haplo.score.merge: Merge haplo.score And haplo.group Objects
haplo.score.slide: Score Statistics for Association of Traits with Haplotypes
hapPower.demo: Set of haplotypes and frequencies for power and sample size...
hla.demo: HLA Loci and Serologic Response to Measles Vaccination
internalHaploStats: Internal functions for the HaploStats package. See the help...
locator.haplo: Find Location from Mouse Clicks and Print Haplotypes on Plot
locus: Creates an object of class "locus"
louis.info: Louis Information for haplo.glm
na.geno.keep: Remove rows with NA in covariates, but keep genotypes with...
plot.haplo.score: Plot Haplotype Frequencies versus Haplotype Score Statistics
plot.haplo.score.slide: Plot a haplo.score.slide Object
plot.seqhap: Plot a seqhap object
printBanner: Print a nice banner
print.haplo.cc: Print a haplo.cc object
print.haplo.em: Print contents of a haplo.em object
print.haplo.group: Print a haplo.group object
print.haplo.scan: Print a haplo.scan object
print.haplo.score: Print a haplo.score object
print.haplo.score.merge: Print a haplo.score.merge object
print.haplo.score.slide: Print the contents of a haplo.score.slide object
residuals.haplo.glm: Accessing residuals for haplo.glm fit
score.sim.control: Create the list of control parameters for simulations in...
seqhap: Sequential Haplotype Scan Association Analysis for...
seqhap.dat: Simulated data for seqhap examples
setupGeno: Create a group of locus objects from a genotype matrix,...
summaryGeno: Summarize Full Haplotype Enumeration on Genotype Matrix
summary.haplo.em: Summarize contents of a haplo.em object
summary.haplo.glm: Print and summary of a haplo.glm object
vcov.haplo.glm: variance-covariance matrix of a fitted haplo.glm object
x.sexcheck: consistency checks for x.linked locus

Functions

Ginv Man page Source code
anova.haplo.glm Man page Source code
anova.haplo.glmlist Man page Source code
chisq.power Man page Source code
chisq.power.dif Man page Source code
chisq.sample.size Man page Source code
dglm.fit Man page Source code
f.power Man page Source code
f.power.dif Man page Source code
f.sample.size Man page Source code
find.beta.qt.phase.known Man page Source code
find.haplo.beta.qt Man page Source code
find.intercept.logistic Man page Source code
find.intercept.qt.phase.known Man page Source code
fitted.haplo.glm Man page Source code
geno.count.pairs Man page Source code
geno1to2 Man page Source code
get.hapPair Man page Source code
hapPower.demo Man page
haplo.binomial Man page Source code
haplo.cc Man page Source code
haplo.chistat Man page Source code
haplo.design Man page Source code
haplo.em Man page Source code
haplo.em.control Man page Source code
haplo.em.fitter Man page Source code
haplo.enum Man page Source code
haplo.glm Man page Source code
haplo.glm.control Man page Source code
haplo.group Man page Source code
haplo.hash Man page Source code
haplo.model.frame Man page Source code
haplo.power.cc Man page Source code
haplo.power.cc.ncp Man page Source code
haplo.power.qt Man page Source code
haplo.power.qt.ncp Man page Source code
haplo.scan Man page Source code
haplo.scan.obs Man page Source code
haplo.scan.sim Man page Source code
haplo.score Man page Source code
haplo.score.glm Man page Source code
haplo.score.merge Man page Source code
haplo.score.podds Man page Source code
haplo.score.slide Man page Source code
hla.demo Man page
locator.haplo Man page Source code
locus Man page Source code
louis.info Man page Source code
mf.gindx Man page Source code
na.geno.keep Man page Source code
onUnload Source code
plot.haplo.score Man page Source code
plot.haplo.score.slide Man page Source code
plot.seqhap Man page Source code
print.haplo.cc Man page Source code
print.haplo.em Man page Source code
print.haplo.glm Man page Source code
print.haplo.group Man page Source code
print.haplo.scan Man page Source code
print.haplo.score Man page Source code
print.haplo.score.merge Man page Source code
print.haplo.score.slide Man page Source code
print.seqhap Man page Source code
print.summary.haplo.glm Man page Source code
printBanner Man page Source code
residScaledGlmFit Man page Source code
residuals.haplo.glm Man page Source code
score.sim.control Man page Source code
seqhap Man page Source code
seqhap.dat Man page
seqhap.pos Man page
setupGeno Man page Source code
sr.class Man page
sr.class<- Man page
summary.haplo.em Man page Source code
summary.haplo.glm Man page Source code
summaryGeno Man page Source code
varfunc.glm.fit Man page Source code
vcov.haplo.glm Man page Source code
x.sexcheck Man page Source code

Files

inst
inst/NEWS.Rd
inst/LICENSE.note
inst/doc
inst/doc/manualHaploStats.pdf
inst/doc/GPL.txt
inst/doc/manualHaploStats.pdf.asis
tests
tests/snapData.csv
tests/test.haplo.em.R
tests/test.haplo.em.Rout.save
tests/test.haplo.cc.R
tests/test.haplo.power.R
tests/test.haplo.power.Rout.save
tests/snap.sim.phased.dat
tests/dump.varx.s
tests/snapFUN.s
tests/test.haplo.cc.Rout.save
src
src/haplo_em_pin.c
src/louis_info.c
src/haplo_em_pin.h
src/groupsum.c
src/seqhap.c
NAMESPACE
data
data/hla.demo.tab.gz
data/seqhap.dat.tab.gz
data/hapPower.demo.tab.gz
data/seqhap.pos.tab.gz
R
R/print.haplo.glm.q
R/summary.haplo.glm.q
R/plot.seqhap.q
R/residScaledGlmFit.q
R/find.haplo.beta.qt.q
R/anova.haplo.glm.q
R/print.haplo.cc.q
R/locator.haplo.q
R/louis.info.q
R/print.haplo.score.slide.q
R/haplo.scan.sim.q
R/haplo.design.q
R/haplo.hash.q
R/haplo.scan.q
R/printBanner.q
R/haplo.score.merge.q
R/varfunc.glm.fit.q
R/haplo.model.frame.q
R/mf.gindx.q
R/get.hapPair.q
R/seqhap.q
R/haplo.cc.q
R/haplo.em.q
R/haplo.binomial.R
R/haplo.chistat.q
R/residuals.haplo.glm.q
R/haplo.power.qt.q
R/x.sexcheck.q
R/print.haplo.scan.q
R/zzz.haplo.stats.R
R/haplo.power.cc.q
R/geno.count.pairs.q
R/plot.haplo.score.q
R/haplo.scan.obs.q
R/summary.haplo.em.q
R/chisq.power.q
R/f.power.q
R/print.haplo.score.merge.q
R/haplo.enum.q
R/print.haplo.group.q
R/print.seqhap.q
R/print.haplo.score.q
R/score.sim.control.q
R/haplo.em.control.q
R/haplo.score.glm.q
R/haplo.score.slide.q
R/plot.haplo.score.slide.q
R/summaryGeno.q
R/locus.q
R/print.haplo.em.q
R/haplo.glm.control.q
R/haplo.em.fitter.q
R/na.geno.keep.q
R/haplo.glm.q
R/geno1to2.q
R/haplo.power.cc.ncp.q
R/dglm.fit.q
R/haplo.power.qt.ncp.q
R/haplo.score.podds.q
R/haplo.score.q
R/setupGeno.q
R/Ginv.R
R/haplo.group.q
vignettes
vignettes/manualHaploStats.pdf.asis
MD5
build
build/vignette.rds
DESCRIPTION
man
man/plot.seqhap.Rd
man/locator.haplo.Rd
man/haplo.scan.Rd
man/f.power.Rd
man/vcov.haplo.glm.Rd
man/find.haplo.beta.qt.Rd
man/chisq.power.Rd
man/fitted.haplo.glm.Rd
man/summary.haplo.glm.Rd
man/print.haplo.score.slide.Rd
man/internalHaploStats.Rd
man/haplo.em.Rd
man/summaryGeno.Rd
man/haplo.em.fitter.Rd
man/print.haplo.cc.Rd
man/plot.haplo.score.slide.Rd
man/haplo.score.slide.Rd
man/print.haplo.scan.Rd
man/geno.count.pairs.Rd
man/na.geno.keep.Rd
man/hla.demo.Rd
man/haplo.em.control.Rd
man/print.haplo.score.merge.Rd
man/haplo.power.cc.Rd
man/haplo.hash.Rd
man/plot.haplo.score.Rd
man/summary.haplo.em.Rd
man/print.haplo.em.Rd
man/geno1to2.Rd
man/louis.info.Rd
man/print.haplo.score.Rd
man/anova.haplo.glm.Rd
man/get.hapPair.Rd
man/haplo.design.Rd
man/x.sexcheck.Rd
man/setupGeno.Rd
man/haplo.score.merge.Rd
man/haplo.power.qt.Rd
man/printBanner.Rd
man/seqhap.Rd
man/locus.Rd
man/haplo.score.Rd
man/haplo.model.frame.Rd
man/Ginv.Rd
man/seqhap.dat.Rd
man/haplo.group.Rd
man/residuals.haplo.glm.Rd
man/haplo.cc.Rd
man/haplo.glm.control.Rd
man/score.sim.control.Rd
man/haplo.glm.Rd
man/print.haplo.group.Rd
man/hapPower.demo.Rd
haplo.stats documentation built on May 19, 2017, 6:21 p.m.