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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 |