remove_gaps_groups {bgafun} | R Documentation |
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.
remove_gaps_groups(x,z,gap_fraction=0.6)
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 |
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)