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

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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.

Author
Sinnwell JP, Schaid DJ
Date of publication
2016-04-06 01:10:36
Maintainer
Jason P. Sinnwell <sinnwell.jason@mayo.edu>
License
GPL (>= 2)
Version
1.7.7
URLs

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

Files in this package

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