rcpp_distIUPACmatrix: rcpp_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 parallel fashion.

Usage

rcpp_distIUPACmatrix(dnavector, scoreMatrix, ncores=1)

Arguments

dnavector	as.character(DNAStringSet)
scoreMatrix	scoreMatrix
ncores	number of parallel cores to process pairwise distance calculation [default: 1]

Author(s)

Kristian K Ullrich

See Also

scoreMatrix, distIUPACmatrix, rcpp_distIUPACmatrix_ab, dist.dna

Examples

##load sequence data
data("MySequences", package="distIUPAC")
##load scoring matrix
MyScoreMatrix<-scoreMatrix()
rcpp_distIUPACmatrix(as.character(MySequences[1:10]), MyScoreMatrix, ncores=2)
##change scoring matrix
MyScoreMatrix["A","R"] <- 10.0
##calculate IUPAC distance with altered scoring
rcpp_distIUPACmatrix(as.character(MySequences[1:10]), MyScoreMatrix, ncores=2)

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