The meaning of sample-wide CF.

[Noppol Kobmoo]

Hi,

I'm trying to understand the difference between the two types of concordance factors (sample-wide vs. genome-wide). I'm not very good at math and I struggle to understand the meaning from the theoretical paper of BUCKy (Ané et al. 2007).

sample-wide CF --> ‘‘sample-wide concordance factor’’ of a clade is the proportion of genes in the sample whose true tree contains the clade.

genome-wide CF -->  ‘‘genome-wide’’ concordance factor for a clade is the proportion of genes in the genome for which the clade c is in the true tree.

While I can conceive what the genome-wide CF means, I'm really having the hard time understanding sample-wide CF... In the definition of the sample-wide CF, what does "sample" mean actually?

[Cécile Ané]

The "sample" here is the sample of loci. So for example, in a data set that contains only 2 genes (or 2 loci more generally), the sample-wide concordance factor can only take 3 possible values: 0, 0.5 or 1, depending on whether 0, 1 or 2 of the 2 gene trees truly have the clade. This extreme example (with a very small sample size = very small number of loci) might help to illustrate that the genome-wide concordance factor is usually more interesting than the "sample"-wide CF. I hope it helps!

[Noppol Kobmoo]

Thank you for your answer. I returned to the paper and now I understand better. The sample-wide CF is calculated solely on the sampled genes in the data while the genome-wide CF is calculated from the sample-wide CF, taking into account the fact that the data were drawn from the genome of which all the genes follow the Dirichet distribution. Correct me if I'm wrong.

ในวันที่ วันศุกร์ที่ 23 ตุลาคม ค.ศ. 2020 เวลา 21 นาฬิกา 02 นาที 32 วินาที UTC+7 Cécile Ané เขียนว่า:

[Cécile Ané]

You are right!