I have some confusion regarding the output of orderMarkers when running sex-specific maps.
In the output, all loci have been placed on both the male and the female map. This should not be possible as, for instance, male informative only loci should be able to be placed only on the male map.
Exact marker placement is impossible in many cases as I discussed this in the Lep-Anchor paper with some simulations. Lep-MAP3 will impute marker positions from other markers that are informative. You can get the information about position uncertainty from the map position intervals (calculateIntervals) or from LOD plots (computeLODScores).
Just adding NAs is not solving the problem as the problem is more complex. Depending on your application, you can for example directly use the intervals (Lep-Anchor), make separate male and female maps (informativeMask=1 and informativeMask=2 / informativeMask=13 and informativeMask=23) or use the physical location of the markers in the marker placement (evaluateOrder or usePhysical=1).
Cheers,
Pasi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I am going back to some old results and am still confused over this topic. I will try and rephrase my question.
When I run OrderMarkers with informativeMask=1 / informative Mask=13, I expect to obtain a map with only male positions, as no recombination events from the female parent are being used.
BUT I obtain a map with both male and female position.
How is the female position obtained when running with only male informative markers?
Cheers,
Lorenzo.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
With informativeMask=13, markers where only father or both parents are informative are included. So you have markers that can be used to detect female recombination as well. You can put the recombination parameter for female to zero by recombination2=0.
With informativeMask=1, the female position will always be 0 as no markers informative in female are included.
Cheers,
Pasi
Last edit: Pasi Rastas 2023-10-09
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello Pasi,
I have some confusion regarding the output of orderMarkers when running sex-specific maps.
In the output, all loci have been placed on both the male and the female map. This should not be possible as, for instance, male informative only loci should be able to be placed only on the male map.
Output:
marker_number male_position female_position
7544 0.000 0.000
7543 0.000 0.719
2285 0.000 0.719
1550 0.000 1.439
2674 1.449 1.439
657 1.449 1.439
Expected output:
marker_number male_position female_position
7544 0.000 0.000
7543 0.000 NA #male informative only, not placed on female map
2285 0.000 0.719
1550 NA 1.439 #female informative only, not placed on male map
2674 1.449 1.439
657 1.449 1.439
What am I missing?
Dear Lorenzo,
Thank you for your question.
Exact marker placement is impossible in many cases as I discussed this in the Lep-Anchor paper with some simulations. Lep-MAP3 will impute marker positions from other markers that are informative. You can get the information about position uncertainty from the map position intervals (calculateIntervals) or from LOD plots (computeLODScores).
Just adding NAs is not solving the problem as the problem is more complex. Depending on your application, you can for example directly use the intervals (Lep-Anchor), make separate male and female maps (informativeMask=1 and informativeMask=2 / informativeMask=13 and informativeMask=23) or use the physical location of the markers in the marker placement (evaluateOrder or usePhysical=1).
Cheers,
Pasi
Hello Pasi,
I am going back to some old results and am still confused over this topic. I will try and rephrase my question.
When I run OrderMarkers with informativeMask=1 / informative Mask=13, I expect to obtain a map with only male positions, as no recombination events from the female parent are being used.
BUT I obtain a map with both male and female position.
How is the female position obtained when running with only male informative markers?
Cheers,
Lorenzo.
Dear Lorenzo,
With informativeMask=13, markers where only father or both parents are informative are included. So you have markers that can be used to detect female recombination as well. You can put the recombination parameter for female to zero by recombination2=0.
With informativeMask=1, the female position will always be 0 as no markers informative in female are included.
Cheers,
Pasi
Last edit: Pasi Rastas 2023-10-09