callCodes |
~~function to do ... ~~ |
callCodes,geneSet-method |
Class "geneSet", a class for genetics data |
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<-,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<-,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<-,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<-,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<-,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<-,geneSet-method |
Class "geneSet", a class for genetics data |
summary.LD |
Pairwise linkage disequilibrium between genetic markers. |