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 |