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 |