| callCodes |
~~function to do ... ~~ |
| callCodes,geneSet-method |
Class "geneSet", a class for genetics data |
| callCodes<- |
~~function to do ... ~~ |
| callCodes<-,geneSet-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,geneSet-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 |
| 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,geneSet-method |
Class "geneSet", a class for genetics data |
| head,LD-method |
Class "LD" ~~~ |
| head,LDband-method |
Class "LDband" ~~~ |
| head,LDdist-method |
Wrapper to efficiently store the result from
performing LD calculatations over sliding windows containing markers
within a distance |
| heterozygote |
Flag observations with specific allele patterns |
| heterozygote,geneSet-method |
Class "geneSet", a class for genetics data |
| heterozygote.geneSet |
Flag observations with specific allele patterns |
| homozygote |
Flag observations with specific allele patterns |
| homozygote,geneSet-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,LD-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,geneSet-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,LD-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,geneSet-method |
Class "geneSet", a class for genetics data |
| LD-class |
Class "LD" ~~~ |
| LDband |
Pairwise linkage disequilibrium between genetic markers. |
| LDband,geneSet-method |
Class "geneSet", a class for genetics data |
| LDband-class |
Class "LDband" ~~~ |
| LDband.geneSet |
Pairwise linkage disequilibrium between genetic markers. |
| LDdist |
Pairwise linkage disequilibrium between genetic markers. |
| LDdist,geneSet-method |
Class "geneSet", a class for genetics data |
| LDdist-class |
Wrapper to efficiently store the result from
performing LD calculatations over sliding windows containing markers
within a distance |
| LDdist.geneSet |
Pairwise linkage disequilibrium between genetic markers. |
| LDView |
Textual and graphical display of linkage disequilibrium (LD) objects |
| left |
~~function to do ... ~~ |
| left,LD-method |
Class "LD" ~~~ |
| left,LDband-method |
Class "LDband" ~~~ |
| left,LDdist-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,geneSet-method |
Class "geneSet", a class for genetics data |
| markerInfo<- |
~~function to do ... ~~ |
| markerInfo<-,geneSet-method |
Class "geneSet", a class for genetics data |
| markerNames |
~~function to do ... ~~ |
| markerNames,geneSet-method |
Class "geneSet", a class for genetics data |
| markerSummary |
Generate allele, genotype, or LD summary objects |
| missingCodes |
~~function to do ... ~~ |
| missingCodes,geneSet-method |
Class "geneSet", a class for genetics data |
| missingCodes<- |
~~function to do ... ~~ |
| missingCodes<-,geneSet-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,geneSet-method |
Class "geneSet", a class for genetics data |
| phase<- |
~~function to do ... ~~ |
| phase<-,geneSet-method |
Class "geneSet", a class for genetics data |
| phenotypeFileFormats |
Import genetic data from standard file formats |
| ploidy |
~~function to do ... ~~ |
| ploidy,geneSet-method |
Class "geneSet", a class for genetics data |
| ploidy<- |
~~function to do ... ~~ |
| ploidy<-,geneSet-method |
Class "geneSet", a class for genetics data |
| plot |
Textual and graphical display of linkage disequilibrium (LD) objects |
| plot,LD-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 |
| sampleInfo |
~~function to do ... ~~ |
| sampleInfo,geneSet-method |
Class "geneSet", a class for genetics data |
| sampleInfo<- |
~~function to do ... ~~ |
| sampleInfo<-,geneSet-method |
Class "geneSet", a class for genetics data |
| show,geneSet-method |
Class "geneSet", a class for genetics data |
| show,LD-method |
Class "LD" ~~~ |
| show,LDband-method |
Class "LDband" ~~~ |
| show,LDdist-method |
Wrapper to efficiently store the result from
performing LD calculatations over sliding windows containing markers
within a distance |
| studyInfo |
~~function to do ... ~~ |
| studyInfo,geneSet-method |
Class "geneSet", a class for genetics data |
| studyInfo<- |
~~function to do ... ~~ |
| studyInfo<-,geneSet-method |
Class "geneSet", a class for genetics data |
| summary.LD |
Pairwise linkage disequilibrium between genetic markers. |