top_residues_2_groups {bgafun} | R Documentation |
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
top_residues_2_groups(bga_results,residue_number=20)
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 |
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)]