scoreMatrix: scoreMatrix

In kullrich/distIUPAC: calculates IUPAC distances on Biostrings DNAStringSet and BStringSet objects

Description

This function creates a scoreMatrix object to be used with the distIUPACmatrix function. By default, the score 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

scoreMatrix()

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

distIUPACmatrix, dist.dna

Examples

data("MySequences", package="distIUPAC")
MyScoreMatrix <- scoreMatrix()
MyScoreMatrix["A","R"] <- 10.0
distIUPACmatrix(as.character(MySequences[1:10]), MyScoreMatrix)
MyScoreMatrix["A","R"] <- 0.5
distIUPACmatrix(as.character(MySequences[1:10]), MyScoreMatrix)

kullrich/distIUPAC documentation built on Jan. 9, 2020, 2:50 p.m.