This function creates a iupacMatrix object to be used
with the rcpp_distSTRING function. By default, the iupac matrix
is defined as literal distance obtained from Chang et al. 2017.
(see https://link.springer.com/article/10.1007/s00335-017-9704-9)
iupacMatrix()score matrix
Chang,P. L.,Kopania,E.,Keeble,S.,Sarver,B. A.,Larson, E.,Orth,A.,... & Dean,M. D. (2017). Whole exome sequencing of wild-derived inbred strains of mice improves power to link phenotype and genotype. Mammalian genome,28(9-10),416-425.
iupacMatrix()
#> A C G T R Y S W K M B D H V . - N X
#> A 0.0 1.0 1.0 1.0 0.5 1.0 1.0 0.5 1.0 0.5 -1 -1 -1 -1 -1 -1 -1 -1
#> C 1.0 0.0 1.0 1.0 1.0 0.5 0.5 1.0 1.0 0.5 -1 -1 -1 -1 -1 -1 -1 -1
#> G 1.0 1.0 0.0 1.0 0.5 1.0 0.5 1.0 0.5 1.0 -1 -1 -1 -1 -1 -1 -1 -1
#> T 1.0 1.0 1.0 0.0 1.0 0.5 1.0 0.5 0.5 1.0 -1 -1 -1 -1 -1 -1 -1 -1
#> R 0.5 1.0 0.5 1.0 0.0 1.0 1.0 1.0 1.0 1.0 -1 -1 -1 -1 -1 -1 -1 -1
#> Y 1.0 0.5 1.0 0.5 1.0 0.0 1.0 1.0 1.0 1.0 -1 -1 -1 -1 -1 -1 -1 -1
#> S 1.0 0.5 0.5 1.0 1.0 1.0 0.0 1.0 1.0 1.0 -1 -1 -1 -1 -1 -1 -1 -1
#> W 0.5 1.0 1.0 0.5 1.0 1.0 1.0 0.0 1.0 1.0 -1 -1 -1 -1 -1 -1 -1 -1
#> K 1.0 1.0 0.5 0.5 1.0 1.0 1.0 1.0 0.0 1.0 -1 -1 -1 -1 -1 -1 -1 -1
#> M 0.5 0.5 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 -1 -1 -1 -1 -1 -1 -1 -1
#> B -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1 -1 -1 -1 -1 -1 -1 -1
#> D -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1 -1 -1 -1 -1 -1 -1 -1
#> H -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1 -1 -1 -1 -1 -1 -1 -1
#> V -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1 -1 -1 -1 -1 -1 -1 -1
#> . -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1 -1 -1 -1 -1 -1 -1 -1
#> - -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1 -1 -1 -1 -1 -1 -1 -1
#> N -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1 -1 -1 -1 -1 -1 -1 -1
#> X -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1 -1 -1 -1 -1 -1 -1 -1