Phased or Unphased Linkage Disequilibrium
Calculation of the , , and conditional Asymmetric LD Measures
Extract Locus Information from Supplied Haplotype Data
Generates heat-maps for four linkage disequilibrium (LD) values (D', W...
Perform the sign test on paired LD values for phased and unphased hapl...
Parser for CSV-formatted GL String Haplotype Data
Reformat columnnar genotype data to GL String format
Truncate allele names in haplotypes to the specified number of fields.
Exporting Haplotype Vectors
Computes the D', Wn, and conditional asymmetric linkage disequilibrium (ALD) measures for pairs of genetic loci. Performs these linkage disequilibrium (LD) calculations on phased genotype data recorded using Genotype List (GL) String or columnar formats. Alternatively, generates expectation-maximization (EM) estimated haplotypes from phased data, or performs LD calculations on EM estimated haplotypes. Performs sign tests comparing LD values for phased and unphased datasets, and generates heat-maps for each LD measure. Described by Osoegawa et al. (2019a) <doi:10.1016/j.humimm.2019.01.010>, and Osoegawa et. al. (2019b) <doi:10.1016/j.humimm.2019.05.018>.