Entry: Ginv
Aliases: Ginv
Keywords: 
Description: Compute Generalized Inverse of Input Matrix
URL: ../../../library/haplo.stats/html/Ginv.html

Entry: allele.recode
Aliases: allele.recode
Keywords: 
Description: Recode allele values to integer ranks
URL: ../../../library/haplo.stats/html/allele.recode.html

Entry: dglm.fit
Aliases: dglm.fit
Keywords: 
Description: Density function for GLM fit
URL: ../../../library/haplo.stats/html/dglm.fit.html

Entry: geno.count.pairs
Aliases: geno.count.pairs
Keywords: 
Description: Counts of Total Haplotype Pairs Produced by Genotypes
URL: ../../../library/haplo.stats/html/geno.count.pairs.html

Entry: geno.recode
Aliases: geno.recode
Keywords: 
Description: Recode Genotypes
URL: ../../../library/haplo.stats/html/geno.recode.html

Entry: glm.fit.nowarn
Aliases: glm.fit.nowarn
Keywords: 
Description: Modified from glm.fit function to not warn users for binomial non-integer weights.
URL: ../../../library/haplo.stats/html/glm.fit.nowarn.html

Entry: haplo.cc
Aliases: haplo.cc
Keywords: 
Description: Haplotype Association Analysis in a Case-Control design
URL: ../../../library/haplo.stats/html/haplo.cc.html

Entry: haplo.chistat
Aliases: haplo.chistat
Keywords: 
Description: Calculate a score test statistic for haplotypes
URL: ../../../library/haplo.stats/html/haplo.chistat.html

Entry: haplo.em
Aliases: haplo.em
Keywords: 
Description: EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
URL: ../../../library/haplo.stats/html/haplo.em.html

Entry: haplo.em.control
Aliases: haplo.em.control
Keywords: 
Description: Create the Control Parameters for the EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
URL: ../../../library/haplo.stats/html/haplo.em.control.html

Entry: haplo.em.fitter
Aliases: haplo.em.fitter
Keywords: 
Description: Compute engine for haplotype EM algorithm
URL: ../../../library/haplo.stats/html/haplo.em.fitter.html

Entry: haplo.enum
Aliases: haplo.enum
Keywords: 
Description: Enumerate all possible pairs of haplotypes that are consistent with a set of un-phased multilocus markers
URL: ../../../library/haplo.stats/html/haplo.enum.html

Entry: haplo.glm
Aliases: haplo.glm
Keywords: 
Description: GLM Regression of Trait on Ambiguous Haplotypes
URL: ../../../library/haplo.stats/html/haplo.glm.html

Entry: haplo.glm.control
Aliases: haplo.glm.control
Keywords: 
Description: Create list of control parameters for haplo.glm
URL: ../../../library/haplo.stats/html/haplo.glm.control.html

Entry: haplo.group
Aliases: haplo.group
Keywords: 
Description: Frequencies for Haplotypes by Grouping Variable
URL: ../../../library/haplo.stats/html/haplo.group.html

Entry: haplo.hash
Aliases: haplo.hash
Keywords: 
Description: Integer Rank Codes for Haplotypes
URL: ../../../library/haplo.stats/html/haplo.hash.html

Entry: haplo.model.frame
Aliases: haplo.model.frame
Keywords: 
Description: Sets up a model frame for haplo.glm
URL: ../../../library/haplo.stats/html/haplo.model.frame.html

Entry: haplo.scan
Aliases: haplo.scan
Keywords: 
Description: Search for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window
URL: ../../../library/haplo.stats/html/haplo.scan.html

Entry: haplo.scan.obs
Aliases: haplo.scan.obs
Keywords: 
Description: For observed data, slide a fixed-width window over each marker locus and scan all possible haplotypes within the window
URL: ../../../library/haplo.stats/html/haplo.scan.obs.html

Entry: haplo.scan.sim
Aliases: haplo.scan.sim
Keywords: 
Description: For simulated data, slide a fixed-width window over each marker locus and scan all possible haplotypes within the window
URL: ../../../library/haplo.stats/html/haplo.scan.sim.html

Entry: haplo.score
Aliases: haplo.score
Keywords: 
Description: Score Statistics for Association of Traits with Haplotypes
URL: ../../../library/haplo.stats/html/haplo.score.html

Entry: haplo.score.glm
Aliases: haplo.score.glm
Keywords: 
Description: Compute haplotype score statistics for GLM
URL: ../../../library/haplo.stats/html/haplo.score.glm.html

Entry: haplo.score.merge
Aliases: haplo.score.merge
Keywords: 
Description: Merge haplo.score And haplo.group Objects
URL: ../../../library/haplo.stats/html/haplo.score.merge.html

Entry: haplo.score.podds
Aliases: haplo.score.podds
Keywords: 
Description: Compute Haplotype Score Statistics for Ordinal Traits with Proportional Odds Model
URL: ../../../library/haplo.stats/html/haplo.score.podds.html

Entry: haplo.score.slide
Aliases: haplo.score.slide
Keywords: 
Description: Score Statistics for Association of Traits with Haplotypes
URL: ../../../library/haplo.stats/html/haplo.score.slide.html

Entry: hla.demo
Aliases: hla.demo
Keywords: datasets
Description: HLA Loci and Serologic Response to Measles Vaccination.
URL: ../../../library/haplo.stats/html/hla.demo.html

Entry: locator.haplo
Aliases: locator.haplo
Keywords: 
Description: Find Location from Mouse Clicks and Print Haplotypes on Plot
URL: ../../../library/haplo.stats/html/locator.haplo.html

Entry: loci
Aliases: loci
Keywords: 
Description: Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.
URL: ../../../library/haplo.stats/html/loci.html

Entry: locus
Aliases: locus
Keywords: classes
Description: Creates an object of class "locus"
URL: ../../../library/haplo.stats/html/locus.html

Entry: louis.info
Aliases: louis.info
Keywords: 
Description: Louis Information for haplo.glm
URL: ../../../library/haplo.stats/html/louis.info.html

Entry: mf.gindx
Aliases: mf.gindx
Keywords: 
Description: Model Frame Genotype Index to Account for Missing Data in haplo.glm
URL: ../../../library/haplo.stats/html/mf.gindx.html

Entry: na.geno.keep
Aliases: na.geno.keep
Keywords: 
Description: Remove rows with NA in covariates, but keep genotypes with NAs
URL: ../../../library/haplo.stats/html/na.geno.keep.html

Entry: plot.haplo.score
Aliases: plot.haplo.score
Keywords: 
Description: Plot Haplotype Frequencies versus Haplotype Score Statistics
URL: ../../../library/haplo.stats/html/plot.haplo.score.html

Entry: plot.haplo.score.slide
Aliases: plot.haplo.score.slide
Keywords: 
Description: Plot a haplo.score.slide Object
URL: ../../../library/haplo.stats/html/plot.haplo.score.slide.html

Entry: print.haplo.cc
Aliases: print.haplo.cc
Keywords: 
Description: Print a haplo.cc object
URL: ../../../library/haplo.stats/html/print.haplo.cc.html

Entry: print.haplo.em
Aliases: print.haplo.em
Keywords: 
Description: Print contents of a haplo.em object
URL: ../../../library/haplo.stats/html/print.haplo.em.html

Entry: print.haplo.glm
Aliases: print.haplo.glm
Keywords: 
Description: Print a contents of a haplo.glm object
URL: ../../../library/haplo.stats/html/print.haplo.glm.html

Entry: print.haplo.group
Aliases: print.haplo.group
Keywords: 
Description: Print a haplo.group object
URL: ../../../library/haplo.stats/html/print.haplo.group.html

Entry: print.haplo.scan
Aliases: print.haplo.scan
Keywords: 
Description: Print a haplo.scan object
URL: ../../../library/haplo.stats/html/print.haplo.scan.html

Entry: print.haplo.score
Aliases: print.haplo.score
Keywords: 
Description: Print a haplo.score object
URL: ../../../library/haplo.stats/html/print.haplo.score.html

Entry: print.haplo.score.merge
Aliases: print.haplo.score.merge
Keywords: 
Description: Print a haplo.score.merge object
URL: ../../../library/haplo.stats/html/print.haplo.score.merge.html

Entry: print.haplo.score.slide
Aliases: print.haplo.score.slide
Keywords: 
Description: Print the contents of a haplo.score.slide object
URL: ../../../library/haplo.stats/html/print.haplo.score.slide.html

Entry: printBanner
Aliases: printBanner
Keywords: 
Description: Print a nice banner
URL: ../../../library/haplo.stats/html/printBanner.html

Entry: residScaledGlmFit
Aliases: residScaledGlmFit
Keywords: 
Description: Scaled Residuals for GLM fit
URL: ../../../library/haplo.stats/html/residScaledGlmFit.html

Entry: score.sim.control
Aliases: score.sim.control
Keywords: 
Description: Create the list of control parameters for simulations in haplo.score
URL: ../../../library/haplo.stats/html/score.sim.control.html

Entry: setupData
Aliases: setupData
Keywords: 
Description: Set up an example dataset provided within the library.
URL: ../../../library/haplo.stats/html/setupData.html

Entry: setupGeno
Aliases: setupGeno
Keywords: 
Description: Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.
URL: ../../../library/haplo.stats/html/setupGeno.html

Entry: summary.haplo.em
Aliases: summary.haplo.em
Keywords: 
Description: Summarize contents of a haplo.em object
URL: ../../../library/haplo.stats/html/summary.haplo.em.html

Entry: summaryGeno
Aliases: summaryGeno
Keywords: 
Description: Summarize Full Haplotype Enumeration on Genotype Matrix
URL: ../../../library/haplo.stats/html/summaryGeno.html

Entry: varfunc.glm.fit
Aliases: varfunc.glm.fit
Keywords: 
Description: Variance Function for GLM
URL: ../../../library/haplo.stats/html/varfunc.glm.fit.html
