convert_aln_amino: Converts an alignment object into binary amino matrix

In bgafun: BGAfun A method to identify specifity determining residues in protein families

Description

Converts an alignment object, read in by the seqinr package, into a binary matrix. The binary matrix represents the absence or presence of amino acids at each position in the alignment

Usage

 convert_aln_amino(Alignment)

Arguments

Alignment

Alignment object read in using read.alignment function in seqinr

Examples

library(bgafun)
LDH <- read.alignment(file = system.file("sequences/LDH-MDH-PF00056.fasta", package = "bgafun"), format = "fasta")
LDH.amino=convert_aln_amino(LDH)
dim(LDH.amino)

Example output

Loading required package: made4
Loading required package: ade4
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: scatterplot3d
Loading required package: seqinr
[1]   45 3600

bgafun documentation built on April 28, 2020, 7:56 p.m.