FreqMat: Matrix of nucleotide or amino acid frequencies in alignment...
In VHIRHepatiques/QSutils: Quasispecies Diversity

FreqMat

R Documentation

Matrix of nucleotide or amino acid frequencies in alignment by position

Description

Computes the nucleotide or amino acid frequency at each position in the alignment.

Usage

FreqMat(seqs,nr=NULL)

Arguments

`seqs`	DNAStringSet or AAStringSet with the aligned haplotype sequences.
`nr`	An optional numeric vector with the haplotype counts.

Value

Matrix with the frequency of each nucleotide or amino acid in each position. A (4 x n) or (20 x n) matrix, where n is the alignment length.

Author(s)

Mercedes Guerrero-Murillo and Josep Gregori

Examples

filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")

# Frequencies only in the alignment.
FreqMat(lst$hseqs)
# Also taking into account haplotype frequencies.
FreqMat(lst$hseqs,lst$nr)

VHIRHepatiques/QSutils documentation built on April 27, 2024, 10:29 p.m.