top_residues_2_groups: Return a list of the top residues at either end of the axis

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

Description

This will identify the residues that are most discriminating between the two groups, and as such are most likely to be specifity determining resdius It will return a list of the residues at the end of the axis in a bga analysis. It is used when there are two groups. The function create\_profile\_strings can be used to look at the amino acid content in the column that the analysis identifies

Usage

 top_residues_2_groups(bga_results,residue_number=20)

Arguments

bga_results	Results of BGA analysis, either from BGA or run\_between\_pca function
residue_number	Number of positions at each end of the axis to return

Examples

library(bgafun)
data(LDH.groups)
data(LDH.amino.gapless)
LDH.binary.bga=bga(t(LDH.amino.gapless+1),LDH.groups)
top_res=top_residues_2_groups(LDH.binary.bga)
#To tidy up the results
names(top_res)=sub("X","",names(top_res))
# to look at the amino acid content in the alignment 
LDH.profiles=create_profile_strings(LDH.amino.gapless,LDH.groups)
LDH.profiles[, colnames(LDH.profiles) %in% names(top_res)]

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