Yes, you can specify the order that way. The markers are numbered as 1,2, ..., N in the order they are in the linkage file and you can specify the order by giving marker numbers, one number per line, e.g.
1
100
102
And is you use improveOrder=0 then this order (without attempts to improve it) is being evaluated.
Cheers,
Pasi
Last edit: Pasi Rastas 2016-06-29
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi Pasi,
I am also interested in evaluating a specific map order. When I provide evaluateOrder to lep-MAP, how will it evaluate markers which appear in the marker order file but do not appear in the .linkage file provided? For example, if certain markers have been filtered during the filtering step, will lep-MAP still attempt to insert these into the map with all the missing genotypes, if the marker numbers appear in my evaluateOrder file?
Thanks!
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Yes, the markers that have been filtered do not matter, but LM2 will not include them in the maps. Those markers are read but not included as they are not informative.
Cheers,
Pasi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi!
I want to estimate a map with for a specific marker order:
evaluateOrder=file
What is the appropriate format for the input file for the evaluateOrder command?
Also, Im assuming that i can constrain the order by using the imporveOrder=0. Is that correct?
Thanks in advance. And great peice of software!
Dear Sean,
Thank you for your question.
Yes, you can specify the order that way. The markers are numbered as 1,2, ..., N in the order they are in the linkage file and you can specify the order by giving marker numbers, one number per line, e.g.
1
100
102
And is you use improveOrder=0 then this order (without attempts to improve it) is being evaluated.
Cheers,
Pasi
Last edit: Pasi Rastas 2016-06-29
Hi Pasi,
I am also interested in evaluating a specific map order. When I provide evaluateOrder to lep-MAP, how will it evaluate markers which appear in the marker order file but do not appear in the .linkage file provided? For example, if certain markers have been filtered during the filtering step, will lep-MAP still attempt to insert these into the map with all the missing genotypes, if the marker numbers appear in my evaluateOrder file?
Thanks!
Dear John,
This is a good question.
Yes, the markers that have been filtered do not matter, but LM2 will not include them in the maps. Those markers are read but not included as they are not informative.
Cheers,
Pasi