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larssnip / micropan

R package for microbial pangenomics
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Interpreting distJacc #16

Closed stephaniesrsouza closed 10 months ago

stephaniesrsouza commented 10 months ago

Hi, I am using distJaccard function and I am wondering about the interpretation of the results.

my input was an accessory genome presence/absence matrix (attached), where each row is one genome and the columns are the genes. 1 means presence/ 0 absence.

My output was the following (just part of it, I did not copy the entire one) "","Var1","Freq" "1","A",0.512974051896208 "2","B",0.423711340206186 "3","C",0.423860329776916 "4","D",0.493881118881119 "5","E",0.687943262411348

I wonder how could I know exactly for each genome pair is the result.

Thanks ST131_acc_genome.csv

stephaniesrsouza commented 10 months ago

Sorry, I realized this table I generated wrongly using some commands and in fact the output is a matrix with the distance for each pair.