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


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allele.recode Recode allele values to integer ranks
dglm.fit Density function for GLM fit
geno.count.pairs Counts of Total Haplotype Pairs Produced by Genotypes
geno.recode Recode Genotypes
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.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 Enumerate all possible pairs of haplotypes that are consistent with a set of un-phased multilocus markers
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.score Score Statistics for Association of Traits with Haplotypes
haplo.score.glm Compute haplotype score statistics for GLM
haplo.score.merge Merge haplo.score And haplo.group Objects
haplo.score.podds Compute Haplotype Score Statistics for Ordinal Traits with Proportional Odds Model
haplo.score.slide Score Statistics for Association of Traits with Haplotypes
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 Model Frame Genotype Index to Account for Missing Data in haplo.glm
na.geno.keep Find non-missing rows in the genotype matrix of the model.frame
plot.haplo.score Plot Haplotype Frequencies versus Haplotype Score Statistics
plot.haplo.score.slide Plot a haplo.score.slide 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.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
printBanner Print a nice banner
residScaledGlmFit Scaled Residuals for GLM fit
score.sim.control Create the list of control parameters for simulations in haplo.score
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.
summary.haplo.em Summarize contents of a haplo.em object
summaryGeno Summarize Full Haplotype Enumeration on Genotype Matrix
varfunc.glm.fit Variance Function for GLM