Population Genetics
Experimental Function to Correct Confidence Intervals At or Near Bound...
Depreciated functions
Estimate or Compute Confidence Interval for the Single-Marker Disequil...
Construct expected genotypes/haplotypes according to known allele vari...
Genotype or Haplotype Objects.
Group genotype values
Extract Features of Genotype objects
Perform Chi-Square Test for Hardy-Weinberg Equilibrium
Exact Test of Hardy-Weinberg Equilibrium for 2-Allele Markers
Estimate Disequilibrium and Test for Hardy-Weinberg Equilibrium
Pairwise linkage disequilibrium between genetic markers.
Create and Manipulate Locus, Gene, and Marker Objects
Convert columns in a dataframe to genotypes or haplotypes
Order/sort genotype/haplotype object
Plot genotype object
Textual and graphical display of linkage disequilibrium (LD) objects
Allele and Genotype Frequency from a Genotype or Haplotype Object
Undocumented functions
Create genetics data files
Classes and methods for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...