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 paramter and pedigree files, checks that they are readable and then outputs the checked files.
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 one catchall unseen alleles that has the total frequency of the original unseen alleles.
Dummy
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.
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.
HaploFreqs	This program find all the haplotypes with frequency above a specified threshold for a graphical model for linkage disequilibrium.
MaxTwoPointLods	This program finds the maximum lod score for values of the recombination between 0 and 1 (not 0 and 0.5).
McLink	This program implements the methods of Thomas, A., Gutin, A., Abkevich, V.
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.
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.
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.

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.