Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
Analysis of variance for haplo.glm model fit
Power and sample size for the chi-square distribution
Power and sample size for the F distribution
Find beta coefficients for risk haplotypes, for specified r2
Fitted values from haplo.glm fit
Counts of Total Haplotype Pairs Produced by Genotypes
convert genotype matrix from 1-column 2-column
Get a list of objects for haplotype pairs
Compute Generalized Inverse of Input Matrix
Haplotype Association Analysis in a Case-Control design
Build a design matrix for haplotypes
Create the Control Parameters for the EM Computation of Haplotype Prob...
Compute engine for haplotype EM algorithm
EM Computation of Haplotype Probabilities, with Progressive Insertion ...
Create list of control parameters for haplo.glm
GLM Regression of Trait on Ambiguous Haplotypes
Frequencies for Haplotypes by Grouping Variable
Integer Rank Codes for Haplotypes
Sets up a model frame for haplo.glm
Compute either power or sample size for haplotype associations in a ca...
Compute either power or sample size for haplotype associations with a ...
Search for a trait-locus by sliding a fixed-width window over each mar...
Merge haplo.score And haplo.group Objects
Score Statistics for Association of Traits with Haplotypes
Score Statistics for Association of Traits with Haplotypes
Set of haplotypes and frequencies for power and sample size calculatio...
HLA Loci and Serologic Response to Measles Vaccination
Internal functions for the HaploStats package. See the help file for t...
Find Location from Mouse Clicks and Print Haplotypes on Plot
Creates an object of class "locus"
Louis Information for haplo.glm
Remove rows with NA in covariates, but keep genotypes with NAs
Plot Haplotype Frequencies versus Haplotype Score Statistics
Plot a haplo.score.slide Object
Plot a seqhap object
Print a haplo.cc object
Print contents of a haplo.em object
Print a haplo.group object
Print a haplo.scan object
Print a haplo.score.merge object
Print a haplo.score object
Print the contents of a haplo.score.slide object
Print a nice banner
Accessing residuals for haplo.glm fit
Create the list of control parameters for simulations in haplo.score
Simulated data for seqhap examples
Sequential Haplotype Scan Association Analysis for Case-Control Data
Create a group of locus objects from a genotype matrix, assign to 'mod...
Summarize contents of a haplo.em object
Print and summary of a haplo.glm object
Summarize Full Haplotype Enumeration on Genotype Matrix
variance-covariance matrix of a fitted haplo.glm object
consistency checks for x.linked locus
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.