iupacMatrix: iupacMatrix

In kullrich/MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

iupacMatrix

Description

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)

Usage

iupacMatrix()

Value

score matrix

Author(s)

Kristian K Ullrich

References

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.

See Also

dnastring2dist,dist.dna

Examples

iupacMatrix()

kullrich/MSA2dist documentation built on Nov. 14, 2024, 5:39 p.m.