Suppose I have reads from 2 species and I assembled the reads into contigs. Then suppose I binned the contigs into 2 clusters, cluster1 and cluster2. And suppose the image below is the result of binned contigs.(supposing I know which contig derived from which species)
species1 species2
cluster1 50 1000
cluster2 150 10
What is the precision and recall respectively in this case?
Is precision = (150+1000)/(1000+150+50+10)?
I've searched the definition of precision and recall here https://en.wikipedia.org/wiki/Precision_and_recall,
and I'm not sure if there is true negative and false negative in this case.
At https://www.nature.com/articles/nmeth.3103, which is a paper on binning contigs, it says recall is the proportion of each species binned to the same cluser. What does the same cluster mean in this case?
Do I have to solve for each species its recall(50/(150+50), 1000/(1000+10) respectively) and get an average?
While searching through the internet, I've found precision and recall in clutering at https://stats.stackexchange.com/questions/15158/precision-and-recall-for-clustering Is this the definition I should apply for each pair of contigs?
Thank you very much.
