FreqMat: Matrix of nucleotide or amino acid frequencies in alignment...

In VHIRHepatiques/QSutils: Quasispecies Diversity

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 12, 2024, 12:25 p.m.