Hello, I am trying to implement PSMC in some analyses I with dummy data to fully understand how does this software work.
However, I am really struggling to understand what does the -p parameter mean. Normally, when you call psmc, you can do it like:
psmc -N10 -t5 -r1 -p "4+30*2+4+6" -o $name.psmc $name.consensus.psmcfa
These are the explanation that psmc provides for each parameter:
Program: psmc (Pairwise SMC Model)
Version: 0.6.5-r67
Contact: <http://hengli.uservoice.com/>
Usage: psmc [options] input.txt
Options: -p STR pattern of parameters [4+5*3+4]
-t FLOAT maximum 2N0 coalescent time [15]
-N INT maximum number of iterations [30]
-r FLOAT initial theta/rho ratio [4]
-c FILE CpG counts generated by cntcpg [null]
-o FILE output file [stdout]
-i FILE input parameter file [null]
-T FLOAT initial divergence time; -1 to disable [-1]
-b bootstrap (input be preprocessed with split_psmcfa)
-S simulate sequence
-d perform decoding
-D print full posterior probabilities
I know that the -p parameter (4+302+4+6) depends on the distribution of coalescent blocks or the discrete time intervals that the population has a constant size. However, I still don't get how I should create* my -p parameter depending on my population. Could anyone help me or telling me where I can find this information? The Readme from psmc is not very clearfull..
Thank you so much in advance.
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