Package <Unnamed>

This default "Unnamed" package contains all the top level programs.

See:
Description

Class Summary

ApproxGCHap	This program finds approximations to the maximum likelihood estimates of haplotype frequencies from a sample of genotyped individuals.
CheckErrors	This program finds the posterior probabilities of errors for genotypes on individuals in pedigrees given a set of observed genotypes and the pedigree structure.
CheckFormat	This program reads in LINKAGE parameter and pedigree files, checks that they are readable and then outputs the checked files.
CheckParameters	This program reads in a LINKAGE parameter, checks that it is correctly foratted and then outputs the checked file.
CheckPedigree	This program reads in LINKAGE a pedigree file, and checks that the pedigree information is correctly formatted and self consistent.
CheckTriplets	This program checks a pedigree specified by a list of triplets for self consisency and completeness.
cMorgansToTheta	This program reads in a LINKAGE parameter file assuming that the distances between the loci are specified as cMorgans.
DownCodeAlleles	This program reduces the number of alleles in the models for the given genetic loci to include only alleles that appear in the pedigree file plus, optionally, one catchall allele to represent the unseen alleles which has frequency equal to the total frequency of the original unseen alleles.
GCHap	This program finds maximum likelihood estimates of haplotype frequencies from a sample of genotyped individuals.
GeneCountAlleles	This program calculates maximum likelihood estimates of allele frequencies from genotypes observed in individuals related in pedigrees.
GeneDrop	This program uses the multi locus gene drop method to simulate genotypes on a pedigree to match those in the input.
GeneDrops	This program uses the multi locus gene drop method to simulate genotypes on a pedigree to match those in the input.
GetPolymorphisms	This program selects from the input data the marker loci for which at least two alleles are observed.
GMCheck	This is the old name for the program CheckErrors.
HapGraph	This program estimates a graphical model for linkage disequilibrium or allelic associateion from genetic data.
HetCutOff	This program selects from the input data the marker loci for which the heterozygosity score is higher than a given threshold.
Heterozygosities	This program reads in a LINKAGE parameter, and outputs the heterozygosity measure for each locus.
HetLods	This program calculates two point hetlod scores on a grid of points.
HGS	This program calculates the runs of loci at which the selected individuals are all homozygous, but not necessarily for the same allele.
IntervalLD	This program estimates a interval graphed graphical model for linkage disequilibrium between genetic loci.
LinkageToFastPhase	Takes data from LINKAGE format parameter and pedigree files and prepares it for input into the FASTPHASE haplotyping program.
LinkageToPhase	Takes data from LINKAGE format parameter and pedigree files and prepares it for input into the PHASE haplotyping program.
MakeProbands	This programs marks inividuals in a pedigree file as being or not being probands.
MaxTwoPointLods	This program finds the maximum lod score for values of the recombination between 0 and 1 (not 0 and 0.5).
McLink
McLinkLD	This program calculates linkage statistics while jointly estimating a model for linkage disequilibrium between the loci.
ObligateErrors	This program checks genotype data on pedigrees and indicates whether the data at any particular locus is inconsistent with Mendelian inheritance.
OnePoints	This program calculates the log likelihood for the data for each pedigree at each locus specified in the input.
SelectKindreds	This program selects a subset of kindreds from a LINKAGE pedigree file.
SelectLoci	This program selects a subset of loci from LINKAGE parameter and pedigree files.
SelectPedigrees	Another name for the SelectKindreds program.
SGS	This program calculates the runs of heterozygous sharing for a set of individuals in a pedigree.
SimHGS	This program performs multi locus gene drop simulations in order to assess the distribution of the length of regions of homozygosity, as calculated by HGS .
SimSGS	This program performs multi locus gene drop simulations in order to assess the distribution of the length of heterozygously shared genomic regions, as calculated by SGS .
TrimPed	This program removes individuals from the pedigree unless they have a minimum number of loci at least partially observed or they are ancestors of someone else that is observed.
TwoPointLods	This program calculates two point lod scores on a grid of points.
ViewGraph	This is and interactive graphical program for viewing and editing a graph.
ViewLinkPed	This is an interactive graphical program for viewing pedigree data.
ViewPed	This is an interactive graphical program for viewing pedigree data.
ZeroLoopPed	This program generates random zero loop pedigrees with specified numbers of marriages and individuals.

Package Description

This default "Unnamed" package contains all the top level programs. These are the only programs that a user needs to know about unless they are writing their own programs using the packages that underlies them.