Exclude similar loci

[Lara]

Hi Dr. Broman and the R/QTL community,

I noticed there is a feature in JoinMap where you can exclude similar loci. I have 1265 loci that are 100% similar and would like to exclude one from each identical pair. Is there a command that can identify the identicals and drop one in R/QTL?

Thanks!

[havi...@umn.edu]

Hi Lara,

This function in R/qtlTools has the capacity.

https://github.com/jtlovell/qtlTools/blob/master/R/dropSimilarMarkers.R

Cheers,

Josh

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Joshua Havill

612-836-7834

On Apr 6, 2022, at 8:57 PM, Lara <ljbri...@gmail.com> wrote:

Hi Dr. Broman and the R/QTL community,

I noticed there is a feature in JoinMap where you can exclude similar loci. I have 1265 loci that are 100% similar and would like to exclude one from each identical pair. Is there a command that can identify the identicals and drop one in R/QTL?

Thanks!

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[Karl Broman]

A related R/qtl function is findDupMarkers(), which looks for markers with identical genotype data. 

And then drop.markers() to remove them.

karl

[Lara]

Thank you both, this is helpful.