data_file_3.txt (0.35 kB)
New-gene matrix in R
This code takes a binary gene matrix of 1s and 0s from QuartetS (ortholog prediction from amino acid FASTA files) output
and sequentially adds each column, counting each row with the addition of a new
1. The process is repeated 1,000 times, each time the order of the
columns being permuted. The output is a matrix in R where the variation
of each permutation is contained in each row. A new-gene curve can
then be plotted by calculating the median of each column and
incorporating variation into the curve by including all values.