distIUPACmatrix: distIUPACmatrix

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

Description

This function calculates scaled pairwise IUPAC distances on Biostrings DNAStringSet and BStringSet objects using a specific scoreMatrix in a sequential fashion.

Usage

distIUPACmatrix(dnavector, scoreMatrix)

Arguments

dnavector	as.character(DNAStringSet)
scoreMatrix	scoreMatrix

Author(s)

Kristian K Ullrich

See Also

scoreMatrix, rcpp_distIUPACmatrix, rcpp_distIUPACmatrix_ab dist.dna

Examples

##load sequence data
data("MySequences", package="distIUPAC")
##load scoring matrix
MyScoreMatrix<-scoreMatrix()
distIUPACmatrix(as.character(MySequences[1:10]), MyScoreMatrix)
##change scoring matrix
MyScoreMatrix["A", "R"]<-10.0
##calculate IUPAC distance with altered scoring
distIUPACmatrix(as.character(MySequences[1:10]), MyScoreMatrix)

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