remove_gaps_groups: remove gaps from a binary amino matrix

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

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)

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