data_file_2.txt (0.34 kB)
core-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 all
1s. 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 core-gene curve can
then be plotted by calculating the median of each column and
incorporating variation into the curve by including all values.