Create variants of the distance matrix

distance between two SNPS vectors are over non NA positions where if lenient is FALSE (default), genotype in genome and rnaseq library pileup must match exactly for a distance score of 0. Note that A/T == T/A. If lenient == TRUE, then if the nucleotide is contained in the genotype, then the distance = 0. For example, A == A, A/T, T/A, A/G, G/A, A/C, C/A.

equivalence_class_dist_matrix(lenient = FALSE)

Arguments

lenient

Set to TRUE to consider, for example, A == A, A/T, T/A, A/G, G/A, A/C, C/A for a distance score of 0. Default is FALSE

Value

a symmetric matrix with rownames corresponding to the 16 possible genotypes