remove_gaps_groups {bgafun} | R Documentation |
remove gaps from a binary amino matrix
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)
[Package
bgafun version 1.4.0
Index]