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

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.

AuthorSinnwell JP, Schaid DJ
Date of publication2016-04-06 01:10:36
MaintainerJason P. Sinnwell <sinnwell.jason@mayo.edu>
LicenseGPL (>= 2)
Version1.7.7
http://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software

View on CRAN

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

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

Files

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

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