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.cc |
Haplotype Association Analysis in a Case-Control design |
haplo.chistat |
Calculate a score test statistic 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 |
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.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.scan.obs |
For observed data, slide a fixed-width window over each marker locus and scan all possible haplotypes within the window |
haplo.scan.sim |
For simulated data, slide a fixed-width window over each marker locus and scan all possible haplotypes within the window |
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 |
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 |
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 |
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 |