run_between_pca {bgafun} | R Documentation |
This is a cover function that runs supervised PCA on a matrix that represents an alignment. The matrix can either be a binary matrix (with or without pseudocounts) or one that represents the properties at each position of the alignment
run_between_pca(x,z,y)
x |
Matrix representation of alignment generated by convert\_aln\_amino |
z |
Matrix representation of alignment generated by convert\_aln\_amino or convert\_aln\_AAP |
y |
Vector or factor that shows the group representation for each sequence in the alignment |
library(bgafun) data(LDH) data(LDH.groups) #Used to calculate the sequence weights data(LDH.amino.gapless) data(LDH.aap.ave) #Run the analysis LDH.aap.ave.bga=run_between_pca(LDH.amino.gapless,LDH.aap.ave,LDH.groups) class(LDH.aap.ave.bga) #to visualise the results plot(LDH.aap.ave.bga)