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A B C D E F G H L M N P Q R S T X misc
| alleleCount | ~~function to do ... ~~ |
| alleleCount-method | Class "geneSet", a class for genetics data |
| alleleLevels | ~~function to do ... ~~ |
| alleleLevels-method | Class "geneSet", a class for genetics data |
| alleles | ~~function to do ... ~~ |
| alleles-method | Class "geneSet", a class for genetics data |
| alleleSummary | Summary of allele information |
| ALZH | Sample from National Institute of Mental Health (NIMH) Genetics Initiative Alzheimer's Disease |
| Armitage | Cochran-Armitage test for linear trends in proportions and frequencies |
| Armitage.default | Cochran-Armitage test for linear trends in proportions and frequencies |
| ArmitageTest | Cochran-Armitage test for linear trends in proportions and frequencies |
| as.geneSet | Convert an existing object to a geneSet |
| as.geneSet.data.frame | Convert an existing object to a geneSet |
| as.geneSet.matrix | Convert an existing object to a geneSet |
| binsearch | Binary Search |
| callCodes | ~~function to do ... ~~ |
| callCodes-method | Class "geneSet", a class for genetics data |
| callCodes<- | ~~function to do ... ~~ |
| callCodes<--method | Class "geneSet", a class for genetics data |
| CAMP | Genotype data from the Childhood Asthma Management Program (CAMP) |
| carrier | Flag observations with specific allele patterns |
| carrier-method | Class "geneSet", a class for genetics data |
| carrier.geneSet | Flag observations with specific allele patterns |
| ci.balance | Experimental Function to Correct Confidence Intervals At or Near Boundaries of the Parameter Space by 'Sliding' the Interval on the Quantile Scale. |
| convert | Efficienctly convert strings of characters into integer codes |
| decodeCallCodes | Converts integer codes in a callCodes matrix to character string representations of geneSet. |
| description | ~~function to do ... ~~ |
| description-method | Class "geneSet", a class for genetics data |
| description<- | ~~function to do ... ~~ |
| description<--method | Class "geneSet", a class for genetics data |
| desMarkers | Descriptive statistics for markers |
| diseq | Estimate or Compute Confidence Interval for the Single-Marker Disequilibrium |
| diseq.ci | Estimate or Compute Confidence Interval for the Single-Marker Disequilibrium |
| diseq.inner | Estimate or Compute Confidence Interval for the Single-Marker Disequilibrium |
| dominant | Flag observations with specific allele patterns |
| dominant-method | Class "geneSet", a class for genetics data |
| dominant.geneSet | Flag observations with specific allele patterns |
| errorMetrics | ~~function to do ... ~~ |
| errorMetrics-method | Class "geneSet", a class for genetics data |
| errorMetrics<- | ~~function to do ... ~~ |
| errorMetrics<--method | Class "geneSet", a class for genetics data |
| extractAlleles | functions for extracting allele levels, allele pairs, and allele codes |
| fastGrid | Create a matrix giving all combinations of the elements of x |
| founderGeneSet | Extract founder info from a geneSet object |
| geneSet | Class "geneSet", a class for genetics data |
| geneSet-class | Class "geneSet", a class for genetics data |
| geneSet2Ped | Translate a geneSet object to a ped matrix |
| genotypeCoding | Get genotype coding |
| genotypeCoding.default | Get genotype coding |
| genotypeFileFormats | Import genetic data from standard file formats |
| genotypeLevels | ~~function to do ... ~~ |
| genotypeLevels-method | Class "geneSet", a class for genetics data |
| genotypes | ~~function to do ... ~~ |
| genotypes-method | Class "geneSet", a class for genetics data |
| genotypeSummary | print the summary of genotypes sorted by markers |
| gregorius | Probability of Observing All Alleles with a Given Frequency in a Sample of a Specified Size. |
| haplo.em.w | Wrapper for EM computation of haplotype probabilities, with Progressive Insertion |
| haplo.scan.w | 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 |
| haplo.score.slide.w | Wrapper for haplo.score.slide in haplo.stats package, which is used to identify sub-haplotypes from a group of loci |
| haplo.score.w | 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 |
| hapmapchr22 | Chromosome 22 genotypes from International HapMap project |
| head-method | Class "LD" ~~~ |
| head-method | Class "LDband" ~~~ |
| head-method | Wrapper to efficiently store the result from performing LD calculatations over sliding windows containing markers within a distance |
| head-method | Class "geneSet", a class for genetics data |
| heterozygote | Flag observations with specific allele patterns |
| heterozygote-method | Class "geneSet", a class for genetics data |
| heterozygote.geneSet | Flag observations with specific allele patterns |
| homozygote | Flag observations with specific allele patterns |
| homozygote-method | Class "geneSet", a class for genetics data |
| homozygote.geneSet | Flag observations with specific allele patterns |
| html | Generate summary table files for genotype objects |
| html-method | Class "LD" ~~~ |
| html.GeneticsBaseSummary | Generate summary table files for genotype objects |
| html.LD | Generate summary table files for genotype objects |
| html.markerSummary | Generate summary table files for genotype objects |
| HWE | Test the significances of Hardy-Weinberg Equilibrium (dis)equilibrium statistics |
| HWE-method | Class "geneSet", a class for genetics data |
| HWE.chisq | Hardy-Weinberg Equilibrium Significance test for a biallelic locus |
| HWE.exact | Exact test for Hardy-Weinberg Equilibrium for a biallelic locus |
| latex | Generate summary table files for genotype objects |
| latex-method | Class "LD" ~~~ |
| latex.default | Generate summary table files for genotype objects |
| latex.GeneticsBaseSummary | Generate summary table files for genotype objects |
| latex.LD | Generate summary table files for genotype objects |
| latex.markerSummary | Generate summary table files for genotype objects |
| LD | Pairwise linkage disequilibrium between genetic markers. |
| LD-class | Class "LD" ~~~ |
| LD-method | Class "geneSet", a class for genetics data |
| LDband | Pairwise linkage disequilibrium between genetic markers. |
| LDband-class | Class "LDband" ~~~ |
| LDband-method | Class "geneSet", a class for genetics data |
| LDband.geneSet | Pairwise linkage disequilibrium between genetic markers. |
| LDdist | Pairwise linkage disequilibrium between genetic markers. |
| LDdist-class | Wrapper to efficiently store the result from performing LD calculatations over sliding windows containing markers within a distance |
| LDdist-method | Class "geneSet", a class for genetics data |
| LDdist.geneSet | Pairwise linkage disequilibrium between genetic markers. |
| LDView | Textual and graphical display of linkage disequilibrium (LD) objects |
| left | ~~function to do ... ~~ |
| left-method | Class "LD" ~~~ |
| left-method | Class "LDband" ~~~ |
| left-method | Wrapper to efficiently store the result from performing LD calculatations over sliding windows containing markers within a distance |
| makeMarkerInfo | makeMarkerInfo creates a dataframe of marker information |
| makeTransTable | makeTransTable creates a single translation table of the markers |
| makeTransTableList | makeTransTableList creates a list of translation tables |
| markerFileFormats | Import genetic data from standard file formats |
| markerInfo | ~~function to do ... ~~ |
| markerInfo-method | Class "geneSet", a class for genetics data |
| markerInfo<- | ~~function to do ... ~~ |
| markerInfo<--method | Class "geneSet", a class for genetics data |
| markerNames | ~~function to do ... ~~ |
| markerNames-method | Class "geneSet", a class for genetics data |
| markerSummary | Generate allele, genotype, or LD summary objects |
| missingCodes | ~~function to do ... ~~ |
| missingCodes-method | Class "geneSet", a class for genetics data |
| missingCodes<- | ~~function to do ... ~~ |
| missingCodes<--method | Class "geneSet", a class for genetics data |
| nallele | ~~function to do ... ~~ |
| nallele-method | Class "geneSet", a class for genetics data |
| nmarker | ~~function to do ... ~~ |
| nmarker-method | Class "geneSet", a class for genetics data |
| nobs-method | Class "geneSet", a class for genetics data |
| notes | ~~function to do ... ~~ |
| notes-method | Class "geneSet", a class for genetics data |
| notes<- | ~~function to do ... ~~ |
| notes<--method | Class "geneSet", a class for genetics data |
| ped2geneSet | translate a ped matrix to a geneSet object |
| PerlegenExample | Small example data set from Perlegen |
| PfizerExample | Small example data set from Pfizer |
| PGtables | ~~function to do ... ~~ |
| phase | ~~function to do ... ~~ |
| phase-method | Class "geneSet", a class for genetics data |
| phase<- | ~~function to do ... ~~ |
| phase<--method | Class "geneSet", a class for genetics data |
| phenotypeFileFormats | Import genetic data from standard file formats |
| ploidy | ~~function to do ... ~~ |
| ploidy-method | Class "geneSet", a class for genetics data |
| ploidy<- | ~~function to do ... ~~ |
| ploidy<--method | Class "geneSet", a class for genetics data |
| plot | Textual and graphical display of linkage disequilibrium (LD) objects |
| plot-method | Class "LD" ~~~ |
| plot.LD | Textual and graphical display of linkage disequilibrium (LD) objects |
| print.GeneticsBaseSummary | Generate summary table files for genotype objects |
| print.markerSummary | Generate allele, genotype, or LD summary objects |
| qtlex | Simulated pedigree with genotypes and one qtl covariate |
| read.fbat.phe | Read '.phe' phenotype file data |
| read.pbat.phe | Read '.phe' phenotype file data |
| read.pfizer | ~~function to do ... ~~ |
| read.pfizer.Listing | ~~function to do ... ~~ |
| read.pfizer.Pivot | ~~function to do ... ~~ |
| read.phe | Read '.phe' phenotype file data |
| readGenes | Import genetic data from standard file formats |
| readGenes.fbat.ped | Function to read pedigree file format |
| readGenes.hapmap.ped | Function to read pedigree file format |
| readGenes.pbat.ped | Function to read pedigree file format |
| readGenes.ped | Function to read pedigree file format |
| readGenes.perlegen | Read Perlegen data files. |
| readGenes.pfizer | Read genetics data files that use Pfizer's data format. |
| recessive | Flag observations with specific allele patterns |
| recessive-method | Class "geneSet", a class for genetics data |
| recessive.geneSet | Flag observations with specific allele patterns |
| right | ~~function to do ... ~~ |
| right-method | Class "LD" ~~~ |
| right-method | Class "LDband" ~~~ |
| right-method | Wrapper to efficiently store the result from performing LD calculatations over sliding windows containing markers within a distance |
| sampleInfo | ~~function to do ... ~~ |
| sampleInfo-method | Class "geneSet", a class for genetics data |
| sampleInfo<- | ~~function to do ... ~~ |
| sampleInfo<--method | Class "geneSet", a class for genetics data |
| show-method | Class "LD" ~~~ |
| show-method | Class "LDband" ~~~ |
| show-method | Wrapper to efficiently store the result from performing LD calculatations over sliding windows containing markers within a distance |
| show-method | Class "geneSet", a class for genetics data |
| studyInfo | ~~function to do ... ~~ |
| studyInfo-method | Class "geneSet", a class for genetics data |
| studyInfo<- | ~~function to do ... ~~ |
| studyInfo<--method | Class "geneSet", a class for genetics data |
| summary.LD | Pairwise linkage disequilibrium between genetic markers. |
| tail-method | Class "LD" ~~~ |
| tail-method | Class "LDband" ~~~ |
| tail-method | Wrapper to efficiently store the result from performing LD calculatations over sliding windows containing markers within a distance |
| tail-method | Class "geneSet", a class for genetics data |
| transTables | ~~function to do ... ~~ |
| transTables-method | Class "geneSet", a class for genetics data |
| transTables<- | ~~function to do ... ~~ |
| transTables<--method | Class "geneSet", a class for genetics data |
| txt | Generate summary table files for genotype objects |
| txt.default | Generate summary table files for genotype objects |
| txt.GeneticsBaseSummary | Generate summary table files for genotype objects |
| txt.LD | Generate summary table files for genotype objects |
| txt.markerSummary | Generate summary table files for genotype objects |
| xbat | Simulated pedigree with genotypes and covariates |
| [-method | Class "geneSet", a class for genetics data |
| [[-method | Class "geneSet", a class for genetics data |