bgafun (version 1.34.0)

remove_gaps_groups: remove gaps from a binary amino matrix

Description

This function is used to deal with gaps in the binary amino acid encoding. It will remove positions from a binary amino matrix that contain more a certain fraction of gaps for any group in a column, in the alignment The gap fraction should be between 0 and 1, and can be changed with the gap\_fraction variable.

Usage

remove_gaps_groups(x,z,gap_fraction=0.6)

Arguments

x

Matrix representation of alignment generated by convert\_aln\_amino

z

Vector or factor that shows the group representation for each sequence in the alignment

gap_fraction

Float between 0 and 1 indicating the fraction of gaps in a column before it should be removed

Examples

library(bgafun)
data(LDH)
data(LDH.groups)
LDH.amino=convert_aln_amino(LDH)
dim(LDH.amino)
LDH.amino.gapless=remove_gaps_groups(LDH.amino,LDH.groups,gap_fraction=0.6)
dim(LDH.amino.gapless)