Entry: ALZH
Aliases: ALZH
Keywords: datasets
Description: Sample from National Institute of Mental Health (NIMH) Genetics Initiative Alzheimer's Disease
URL: ../../../library/GeneticsBase/html/ALZH.html

Entry: Armitage
Aliases: Armitage Armitage.default ArmitageTest
Keywords: misc
Description: Cochran-Armitage test for linear trends in proportions and frequencies
URL: ../../../library/GeneticsBase/html/Armitage.html

Entry: CAMP
Aliases: CAMP
Keywords: datasets
Description: Genotype data from the Childhood Asthma Management Program (CAMP)
URL: ../../../library/GeneticsBase/html/CAMP.html

Entry: HWE
Aliases: HWE
Keywords: misc
Description: Test the significances of Hardy-Weinberg Equilibrium (dis)equilibrium) statistics
URL: ../../../library/GeneticsBase/html/HWE.html

Entry: HWE.chisq
Aliases: HWE.chisq
Keywords: misc
Description: Hardy-Weinberg Equilibrium Significance test for a biallelic locus
URL: ../../../library/GeneticsBase/html/HWE.chisq.html

Entry: HWE.exact
Aliases: HWE.exact
Keywords: misc
Description: Exact test for Hardy-Weinberg Equilibrium for a biallelic locus
URL: ../../../library/GeneticsBase/html/HWE.exact.html

Entry: LD-class
Aliases: LD-class head,LD-method html,LD-method latex,LD-method left,LD-method plot,LD-method right,LD-method show,LD-method tail,LD-method
Keywords: classes
Description: Class "LD" ~~~
URL: ../../../library/GeneticsBase/html/LD-class.html

Entry: LD
Aliases: LD LDband LDdist LDband.geneSet LDdist.geneSet summary.LD
Keywords: misc
Description: Pairwise linkage disequilibrium between genetic markers.
URL: ../../../library/GeneticsBase/html/LD.html

Entry: LDband-class
Aliases: LDband-class head,LDband-method left,LDband-method right,LDband-method show,LDband-method tail,LDband-method
Keywords: classes
Description: Class "LDband" ~~~
URL: ../../../library/GeneticsBase/html/LDband-class.html

Entry: LDdist-class
Aliases: LDdist-class head,LDdist-method left,LDdist-method right,LDdist-method show,LDdist-method tail,LDdist-method
Keywords: classes
Description: Wrapper to efficiently store the result from performing LD calculatations over sliding windows containing markers within a distance
URL: ../../../library/GeneticsBase/html/LDdist-class.html

Entry: PGtables
Aliases: PGtables
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/PGtables.html

Entry: PerlegenExample
Aliases: PerlegenExample
Keywords: datasets
Description: Small example data set from Perlegen
URL: ../../../library/GeneticsBase/html/PerlgenExample.html

Entry: PfizerExample
Aliases: PfizerExample
Keywords: datasets
Description: Small example data set from Pfizer
URL: ../../../library/GeneticsBase/html/PfizerExample.html

Entry: alleleCount
Aliases: alleleCount
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/alleleCount.html

Entry: alleleLevels
Aliases: alleleLevels
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/alleleLevels.html

Entry: alleleSummary
Aliases: alleleSummary
Keywords: misc
Description: Summary of allele information
URL: ../../../library/GeneticsBase/html/alleleSummary.html

Entry: alleles
Aliases: alleles
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/alleles.html

Entry: binsearch
Aliases: binsearch
Keywords: optimize programming
Description: Binary Search
URL: ../../../library/GeneticsBase/html/binsearch.html

Entry: callCodes
Aliases: callCodes callCodes<-
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/callCodes.html

Entry: ci.balance
Aliases: ci.balance
Keywords: misc
Description: Experimental Function to Correct Confidence Intervals At or Near Boundaries of the Parameter Space by 'Sliding' the Interval on the Quantile Scale.
URL: ../../../library/GeneticsBase/html/ci.balance.html

Entry: convert
Aliases: convert
Keywords: misc
Description: Efficienctly convert strings of characters into integer codes
URL: ../../../library/GeneticsBase/html/convert.html

Entry: decodeCallCodes
Aliases: decodeCallCodes
Keywords: misc
Description: Converts integer codes in a callCodes matrix to character string representations of geneSet.
URL: ../../../library/GeneticsBase/html/decodeCallCodes.html

Entry: desMarkers
Aliases: desMarkers
Keywords: htest
Description: Descriptive statistics for markers
URL: ../../../library/GeneticsBase/html/desMarkers.html

Entry: description
Aliases: description description<-
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/description.html

Entry: diseq
Aliases: diseq diseq.ci diseq.inner
Keywords: misc
Description: Estimate or Compute Confidence Interval for the Single-Marker Disequilibrium
URL: ../../../library/GeneticsBase/html/diseq.html

Entry: errorMetrics
Aliases: errorMetrics errorMetrics<-
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/errorMetrics.html

Entry: extractAlleles
Aliases: extractAlleles
Keywords: misc
Description: functions for extracting allele levels, allele pairs, and allele codes
URL: ../../../library/GeneticsBase/html/extractAlleles.html

Entry: fastGrid
Aliases: fastGrid
Keywords: misc
Description: Create a matrix giving all combinations of the elements of x
URL: ../../../library/GeneticsBase/html/fastGrid.html

Entry: founderGeneSet
Aliases: founderGeneSet
Keywords: misc
Description: Extract founder info from a geneSet object
URL: ../../../library/GeneticsBase/html/founderGeneSet.html

Entry: geneSet-class
Aliases: geneSet-class geneSet HWE,geneSet-method LD,geneSet-method LDband,geneSet-method LDdist,geneSet-method [,geneSet-method [[,geneSet-method alleleCount,geneSet-method alleleLevels,geneSet-method alleles,geneSet-method callCodes,geneSet-method callCodes<-,geneSet-method carrier,geneSet-method description,geneSet-method description<-,geneSet-method dominant,geneSet-method errorMetrics,geneSet-method errorMetrics<-,geneSet-method genotypeLevels,geneSet-method genotypes,geneSet-method head,geneSet-method heterozygote,geneSet-method homozygote,geneSet-method markerInfo,geneSet-method markerInfo<-,geneSet-method markerNames,geneSet-method missingCodes,geneSet-method missingCodes<-,geneSet-method nallele,geneSet-method nmarker,geneSet-method nobs,geneSet-method notes,geneSet-method notes<-,geneSet-method phase,geneSet-method phase<-,geneSet-method ploidy,geneSet-method ploidy<-,geneSet-method recessive,geneSet-method sampleInfo,geneSet-method sampleInfo<-,geneSet-method show,geneSet-method studyInfo,geneSet-method studyInfo<-,geneSet-method tail,geneSet-method transTables,geneSet-method transTables<-,geneSet-method
Keywords: classes
Description: Class "geneSet", a class for genetics data
URL: ../../../library/GeneticsBase/html/geneSet-class.html

Entry: geneSet2Ped
Aliases: geneSet2Ped
Keywords: misc
Description: Translate a geneSet object to a ped matrix
URL: ../../../library/GeneticsBase/html/geneSet2Ped.html

Entry: genotypeCoding
Aliases: genotypeCoding genotypeCoding.default
Keywords: misc
Description: Get genotype coding
URL: ../../../library/GeneticsBase/html/genotypeCoding.html

Entry: genotypeLevels
Aliases: genotypeLevels
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/genotypeLevels.html

Entry: genotypeSummary
Aliases: genotypeSummary
Keywords: misc
Description: print the summary of genotypes sorted by markers
URL: ../../../library/GeneticsBase/html/genotypeSummary.html

Entry: genotypes
Aliases: genotypes
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/genotypes.html

Entry: gregorius
Aliases: gregorius
Keywords: misc
Description: Probability of Observing All Alleles with a Given Frequency in a Sample of a Specified Size.
URL: ../../../library/GeneticsBase/html/gregorius.html

Entry: haplo.em.w
Aliases: haplo.em.w
Keywords: misc
Description: Wrapper for EM computation of haplotype probabilities, with Progressive Insertion
URL: ../../../library/GeneticsBase/html/haplo.em.w.html

Entry: haplo.scan.w
Aliases: haplo.scan.w
Keywords: misc
Description: Wrapper for searching 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/GeneticsBase/html/haplo.scan.w.html

Entry: haplo.score.slide.w
Aliases: haplo.score.slide.w
Keywords: misc
Description: Wrapper for haplo.score.slide in haplo.stats package, which is used to identify sub-haplotypes from a group of loci
URL: ../../../library/GeneticsBase/html/haplo.score.slide.w.html

Entry: haplo.score.w
Aliases: haplo.score.w
Keywords: misc
Description: Wrapper for computing score statistics to evaluate the association of a trait with haplotypes, when linkage phase is unknown and diploid marker phenotypes are observed among unrelated subjects
URL: ../../../library/GeneticsBase/html/haplo.score.w.html

Entry: hapmapchr22
Aliases: hapmapchr22
Keywords: datasets
Description: Chromosome 22 genotypes from International HapMap project
URL: ../../../library/GeneticsBase/html/hapmapchr.html

Entry: homozygote
Aliases: homozygote homozygote.geneSet heterozygote heterozygote.geneSet carrier carrier.geneSet dominant dominant.geneSet recessive recessive.geneSet
Keywords: misc
Description: Flag observations with specific allele patterns
URL: ../../../library/GeneticsBase/html/homozygote.html

Entry: html
Aliases: html html.LD html.markerSummary html.GeneticsBaseSummary txt txt.default txt.LD txt.markerSummary txt.GeneticsBaseSummary print.GeneticsBaseSummary latex latex.default latex.LD latex.markerSummary latex.GeneticsBaseSummary
Keywords: misc
Description: Generate summary table files for genotype objects
URL: ../../../library/GeneticsBase/html/html.html

Entry: left
Aliases: left right
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/left.html

Entry: makeMarkerInfo
Aliases: makeMarkerInfo
Keywords: misc
Description: makeMarkerInfo creates a dataframe of marker information
URL: ../../../library/GeneticsBase/html/makeMarkerInfo.html

Entry: makeTransTable
Aliases: makeTransTable
Keywords: misc
Description: makeTransTable creates a single translation table of the markers
URL: ../../../library/GeneticsBase/html/makeTransTable.html

Entry: makeTransTableList
Aliases: makeTransTableList
Keywords: misc
Description: makeTransTableList creates a list of translation tables
URL: ../../../library/GeneticsBase/html/makeTransTableList.html

Entry: markerInfo
Aliases: markerInfo markerInfo<-
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/markerInfo.html

Entry: markerNames
Aliases: markerNames
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/markerNames.html

Entry: markerSummary
Aliases: markerSummary print.markerSummary
Keywords: misc
Description: Generate allele, genotype, or LD summary objects
URL: ../../../library/GeneticsBase/html/markerSummary.html

Entry: missingCodes
Aliases: missingCodes missingCodes<-
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/missingCodes.html

Entry: nallele
Aliases: nallele
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/nallele.html

Entry: nmarker
Aliases: nmarker
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/nmarker.html

Entry: notes
Aliases: notes notes<-
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/notes.html

Entry: ped2geneSet
Aliases: ped2geneSet
Keywords: misc
Description: translate a ped matrix to a geneSet object
URL: ../../../library/GeneticsBase/html/ped2geneSet.html

Entry: phase
Aliases: phase phase<-
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/phase.html

Entry: ploidy
Aliases: ploidy ploidy<-
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/ploidy.html

Entry: plot.LD
Aliases: plot.LD plot LDView
Keywords: misc
Description: Textual and graphical display of linkage disequilibrium (LD) objects
URL: ../../../library/GeneticsBase/html/print.LD.html

Entry: qtlex
Aliases: qtlex
Keywords: datasets
Description: Simulated pedigree with genotypes and one qtl covariate
URL: ../../../library/GeneticsBase/html/qtlex.html

Entry: read.pfizer
Aliases: read.pfizer read.pfizer.Listing read.pfizer.Pivot
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/read.pfizer.html

Entry: read.phe
Aliases: read.phe read.fbat.phe read.pbat.phe
Keywords: misc
Description: Read '.phe' phenotype file data
URL: ../../../library/GeneticsBase/html/read.phe.html

Entry: readGenes
Aliases: readGenes genotypeFileFormats phenotypeFileFormats markerFileFormats
Keywords: misc
Description: Import genetic data from standard file formats
URL: ../../../library/GeneticsBase/html/readGenes.html

Entry: readGenes.ped
Aliases: readGenes.ped readGenes.fbat.ped readGenes.pbat.ped readGenes.hapmap.ped
Keywords: misc
Description: Function to read pedigree file format
URL: ../../../library/GeneticsBase/html/readGenes.ped.html

Entry: readGenes.perlegen
Aliases: readGenes.perlegen
Keywords: misc
Description: Read Perlegen data files.
URL: ../../../library/GeneticsBase/html/readGenes.perlegen.html

Entry: readGenes.pfizer
Aliases: readGenes.pfizer
Keywords: misc
Description: Read genetics data files that use Pfizer's data format.
URL: ../../../library/GeneticsBase/html/readGenes.pfizer.html

Entry: sampleInfo
Aliases: sampleInfo sampleInfo<-
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/sampleInfo.html

Entry: studyInfo
Aliases: studyInfo studyInfo<-
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/studyInfo.html

Entry: transTables
Aliases: transTables transTables<-
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/GeneticsBase/html/transTables.html

Entry: xbat
Aliases: xbat
Keywords: datasets
Description: Simulated pedigree with genotypes and covariates
URL: ../../../library/GeneticsBase/html/xbat.html
