Comments (3)
Dear @Ahhgust
Thanks for using our program! Can you take a look at the document at https://cran.r-project.org/web/packages/DEploid/vignettes/dEploid-Arguments.html
Hope this provides some context for using the program R interface. The $Proportions records MCMC samples of the proportion, and please use the last entry as a point estimate.
We fix the number of strains (5 as default), as the deconvolution proceeds, we drop the strains that has proportion below 0.01 (in the final iteration). E.g. if the last proportions are like
0.3. 0.699 1.2e-4 1.2e-4 0.00076
There are then 2 strains with proportions of .3 and .7
Hope this helps!
Best
Joe
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Thanks for getting back to me so quickly!
In your example, I would have inferred two haplotypes and two haplotype frequencies-- how do these values correspond? e.g., how would I know which haplotype was at frequency 0.3? Is the ordering maintained?
from deploid-r.
@Ahhgust Yes, the ordering is maintained.
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