xpclr
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hardingnj
Document which is object and which reference population in command line
Hi, @hardingnj. In the old version(2009) of XP-CLR, it distinguish the genotype1 and genotype2 to object population and reference population, respectively. After apply my data in the new version using VCF format, I notice there are only parameters of -samplesA and -samplesB, I'm wondering which samples represents the reference population (A or B)? Since I didn't find the information in README file, Sincerely hope can get your suggestion. And thanks in advance.
Hi there-
Thanks for the report. A is the object, and B the reference. I appreciate this is unclear in the docs, I'll leave this issue open.
PS Just to be clear- there is no "old" version and "new" version. This is an alternative version, I have had no contact with the original developers.
*edited to correct prev error Aug 2021
Hi, @hardingnj Thanks for your kindly response. There is another question that I want to confirm. For a higher XP-CLR score, if the diversity of reference population will much more higher than the object population? On the other words, will the algorithm assume a higher diversity in reference genome?
A higher XPCLR score suggests the Divergence between the 2 is higher than expected (given the genome wide divergence). Diversity is related but not part of the xpclr score
Hi, @hardingnj It seems weird to ask again about the reference and object population. But I am still having a confusion. In your script I found popA = Pop1 and popB = Pop2. If I compare the codes of c (strength of selection) and Omega in your script with the original article from Hua-Chen 2010, I can see that Pop2 is used as reference population. Can you please confirm. And I also did not understand why allele freq in Pop2 (in your case is popB/ or object population) should be >0 and <1, while Hua-Chen 2010 did not filter in object pop but they filtered in ref population in simulation step. Can you please help? Thanks!
Hi @hardingnj
Could you kindly help us to confirm which option corresponds to the object population (that is the population in which the selection signals registered)?
Best wishes, Zheng zhuqing
Apologies for not being clear on this.
Object is pop A. Reference is pop B. I was mistaken above.
SNPs that are fixed in the reference population are removed because there is no way for the allele frequency to drift from 0 or 1 to another value. As XPCLR relies on identifying much faster than normal drift these sites are not useful (using this method).
Of course, if SNPs are fixed in the object population and not the reference population these sites are informative and therefore included.
Hi @hardingnj
Could you kindly help us to confirm which option corresponds to the object population (that is the population in which the selection signals registered)?
Best wishes, Zheng zhuqing
I want to cofirm again that A or B is the object
Hi @hardingnj
Could you kindly help us to confirm which option corresponds to the object population (that is the population in which the selection signals registered)?
Best wishes, Zheng zhuqing
I want to confirm again that A or B is the object (that is the selected pop), because I have seen many people used A with wild pop and B with clutivar pop when used the python version xpclr . thanks
Hi - I wrote this code a while ago to address a couple of bugs I found in XPCLR in C.
I never really intended for it to be a tool that I support- I just thought I'd share it in case it was useful.
If you have concerns about which population is which- I suggest you take a look at the source and report back here. It's several years since I wrote it and I honestly can't recall.