Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous


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Documentation for package ‘haplo.stats’ version 1.3.8

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allele.recode Internal functions for the HaploStats package
chisq.power Power and sample size for the chi-square distribution
chisq.sample.size Power and sample size for the chi-square distribution
dglm.fit Internal functions for the HaploStats package
f.power Power and sample size for the F distribution
f.sample.size Power and sample size for the F distribution
find.beta.qt.phase.known Find beta's for risk haplotypes, for specified r2
find.haplo.beta.qt Find beta's for risk haplotypes, for specified r2
find.intercept.logistic Compute either power or sample size for haplotype associations in a case-control study.
find.intercept.qt.phase.known Find beta's for risk haplotypes, for specified r2
geno.count.pairs Counts of Total Haplotype Pairs Produced by Genotypes
geno.recode Internal functions for the HaploStats package
geno1to2 convert genotype matrix from 1-column 2-column
get.hapPair Get a list of objects for haplotype pairs
Ginv Compute Generalized Inverse of Input Matrix
glm.fit.nowarn Modified from glm.fit function to not warn users for binomial non-integer weights.
haplo.cc Haplotype Association Analysis in a Case-Control design
haplo.chistat Internal functions for the HaploStats package
haplo.design Build a design matrix for haplotypes
haplo.em EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
haplo.em.control Create the Control Parameters for the EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
haplo.em.fitter Compute engine for haplotype EM algorithm
haplo.enum Internal functions for the HaploStats package
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 associations in a case-control study.
haplo.power.qt Compute either power or sample size for haplotype associations with a quantitative trait.
haplo.scan Search for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window
haplo.score Score Statistics for Association of Traits with Haplotypes
haplo.score.glm Internal functions for the HaploStats package
haplo.score.merge Merge haplo.score And haplo.group Objects
haplo.score.podds Internal functions for the HaploStats package
haplo.score.slide Score Statistics for Association of Traits with Haplotypes
hapPower.demo Set of haplotypes and frequencies for power and sample size calculations
hla.demo HLA Loci and Serologic Response to Measles Vaccination.
locator.haplo Find Location from Mouse Clicks and Print Haplotypes on Plot
loci Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.
locus Creates an object of class "locus"
louis.info Louis Information for haplo.glm
mf.gindx Internal functions for the HaploStats package
na.geno.keep Remove rows with NA in covariates, but keep genotypes with NAs
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
print.haplo.cc Print a haplo.cc object
print.haplo.em Print contents of a haplo.em object
print.haplo.glm Print a contents of a haplo.glm 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
print.seqhap Print Contents of a Seqhap Object
printBanner Print a nice banner
residScaledGlmFit Internal functions for the HaploStats package
score.sim.control Create the list of control parameters for simulations in haplo.score
seqhap Sequential Haplotype Scan Association Analysis for Case-Control Data
seqhap.dat Simulated data for seqhap examples
seqhap.pos Simulated data for seqhap examples
setupData Set up an example dataset provided within the library.
setupGeno Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.
sr.class Internal functions for the HaploStats package
summary.haplo.em Summarize contents of a haplo.em object
summaryGeno Summarize Full Haplotype Enumeration on Genotype Matrix
varfunc.glm.fit Internal functions for the HaploStats package
x.sexcheck consistency checks for x.linked locus