Classes and functions for handling genetic data


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Documentation for package ‘GeneticsBase’ version 1.8.0

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A B C D E F G H L M N P Q R S T X misc

-- A --

alleleCount ~~function to do ... ~~
alleleCount,geneSet-method Class "geneSet", a class for genetics data
alleleLevels ~~function to do ... ~~
alleleLevels,geneSet-method Class "geneSet", a class for genetics data
alleles ~~function to do ... ~~
alleles,geneSet-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
ArmitageTest Cochran-Armitage test for linear trends in proportions and frequencies
as.geneSet Convert an existing object to a geneSet

-- B --

binsearch Binary Search

-- C --

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

-- D --

decodeCallCodes Converts integer codes in a callCodes matrix to character string representations of geneSet.
description ~~function to do ... ~~
description,geneSet-method Class "geneSet", a class for genetics data
description<-,geneSet-method Class "geneSet", a class for genetics data
desMarkers Descriptive statistics for markers
diseq Estimate or Compute Confidence Interval for the Single-Marker Disequilibrium
dominant Flag observations with specific allele patterns
dominant,geneSet-method Class "geneSet", a class for genetics data
dominant.geneSet Flag observations with specific allele patterns

-- E --

errorMetrics ~~function to do ... ~~
errorMetrics,geneSet-method Class "geneSet", a class for genetics data
errorMetrics<-,geneSet-method Class "geneSet", a class for genetics data
extractAlleles functions for extracting allele levels, allele pairs, and allele codes

-- F --

fastGrid Create a matrix giving all combinations of the elements of x
founderGeneSet Extract founder info from a geneSet object

-- G --

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
genotypeFileFormats Import genetic data from standard file formats
genotypeLevels ~~function to do ... ~~
genotypeLevels,geneSet-method Class "geneSet", a class for genetics data
genotypes ~~function to do ... ~~
genotypes,geneSet-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.

-- H --

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

-- L --

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

-- M --

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

-- N --

nallele ~~function to do ... ~~
nallele,geneSet-method Class "geneSet", a class for genetics data
nmarker ~~function to do ... ~~
nmarker,geneSet-method Class "geneSet", a class for genetics data
nobs,geneSet-method Class "geneSet", a class for genetics data
notes ~~function to do ... ~~
notes,geneSet-method Class "geneSet", a class for genetics data
notes<-,geneSet-method Class "geneSet", a class for genetics data

-- P --

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

-- Q --

qtlex Simulated pedigree with genotypes and one qtl covariate

-- R --

read.fbat.phe Read '.phe' phenotype file data
read.pbat.phe Read '.phe' phenotype file data
read.pfizer ~~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,geneSet-method Class "geneSet", a class for genetics data
recessive.geneSet Flag observations with specific allele patterns
right ~~function to do ... ~~
right,LD-method Class "LD" ~~~
right,LDband-method Class "LDband" ~~~
right,LDdist-method Wrapper to efficiently store the result from performing LD calculatations over sliding windows containing markers within a distance

-- S --

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.

-- T --

tail,geneSet-method Class "geneSet", a class for genetics data
tail,LD-method Class "LD" ~~~
tail,LDband-method Class "LDband" ~~~
tail,LDdist-method Wrapper to efficiently store the result from performing LD calculatations over sliding windows containing markers within a distance
transTables ~~function to do ... ~~
transTables,geneSet-method Class "geneSet", a class for genetics data
transTables<-,geneSet-method Class "geneSet", a class for genetics data
txt Generate summary table files for genotype objects

-- X --

xbat Simulated pedigree with genotypes and covariates

-- misc --

[,geneSet-method Class "geneSet", a class for genetics data
[[,geneSet-method Class "geneSet", a class for genetics data