# Classes and functions for handling genetic data

## Documentation for package ‘GeneticsBase’ version 1.2.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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

## -- 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