Turn off recombination

[Anilkumargpb]

Hi Gaynor,

Is it possible to turn off recombination while simulating the population? If possible, please share the function.

Thanks
Anil

[gaynorr]

Hi @Anilkumargpb,

Sorry for not responding earlier.

You can adjust the genetic map at any time in the simulation. Thus, you can effectively turn off recombination by setting all the genetic map positions to 0. The software will still go through the steps of modeling recombination, but there would never be an opportunity for recombination to occur. Note that sampling of chromosomes during meiosis will still occur. Below is some example code.

library(AlphaSimR)

founderPop = quickHaplo(nInd=2, nChr=1, segSites=10, 
                        inbred=TRUE)

# Turning recombination tracking on to be able to use
# pullIbdHaplo
SP = SimParam$
  new(founderPop)$
  setTrackRec(TRUE) 


# Setting all map positions to zero and saving original map
origMap = SP$genMap
zeroMap = lapply(origMap, function(x) x*0)
SP$switchGenMap(zeroMap)

# Create initial parents and make F2s
Parents = newPop(founderPop)
F1 = randCross(Parents, nCrosses=1)
F2 = self(F1, nProgeny=30)

# Examine haplotypes, there will be no recombination
# There should only be rows of 1s and 2s
pullIbdHaplo(Parents)
pullIbdHaplo(F1)
pullIbdHaplo(F2)

# Return to original map and recreate F2s
SP$switchGenMap(origMap)
F2r = self(F1, nProgeny=30)

# You should now see recombinations
pullIbdHaplo(F2r)

[Anilkumargpb]

Hello Chris, Thanks for your response and information on blocking recombinations while simulating. Thanks *डॉ. अनिल कुमार सी Dr. Anilkumar C.* वैज्ञानिक (आनुवंशिकी एवं पौध प्रजनन) Scientist (Genetics & Plant Breeding) फसल उन्नयन प्रभाग Crop Improvement Division भाकृअनुप-राष्ट्रीय चावल अनुसंधान संस्थान, कटक, भारत -753006 ICAR-National Rice Research Institute, Cuttack, Odisha, India -753006 *Fulbright Postdoc Fellow* Dept. of Agronomy and Plant Genetics University of Minnesota, St. Paul, MN, USA <https://www.linkedin.com/in/anilkumar-c-85a4a497/>

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On Tue, Aug 20, 2024 at 7:06 AM Chris Gaynor ***@***.***> wrote: Hi @Anilkumargpb <https://github.com/Anilkumargpb>, Sorry for not responding earlier. You can adjust the genetic map at any time in the simulation. Thus, you can effectively turn off recombination by setting all the genetic map positions to 0. The software will still go through the steps of modeling recombination, but there would never be an opportunity for recombination to occur. Note that sampling of chromosomes during meiosis will still occur. Below is some example code. library(AlphaSimR) founderPop = quickHaplo(nInd=2, nChr=1, segSites=10, inbred=TRUE) # Turning recombination tracking on to be able to use # pullIbdHaplo SP = SimParam$ new(founderPop)$ setTrackRec(TRUE) # Setting all map positions to zero and saving original map origMap = SP$genMap zeroMap = lapply(origMap, function(x) x*0) SP$switchGenMap(zeroMap) # Create initial parents and make F2s Parents = newPop(founderPop) F1 = randCross(Parents, nCrosses=1) F2 = self(F1, nProgeny=30) # Examine haplotypes, there will be no recombination # There should only be rows of 1s and 2s pullIbdHaplo(Parents) pullIbdHaplo(F1) pullIbdHaplo(F2) # Return to original map and recreate F2s SP$switchGenMap(origMap) F2r = self(F1, nProgeny=30) # You should now see recombinations pullIbdHaplo(F2r) — Reply to this email directly, view it on GitHub <#194 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BHKKOSWSB3NICJIUN4IFU43ZSMWLFAVCNFSM6AAAAABMBKSEDOVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTAMZZGUZTGNI> . You are receiving this because you were mentioned.Message ID: ***@***.***>