Something like qtlDesign for multiple parents

Conor Simpson

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Mar 14, 2022, 11:42:25 AM3/14/22

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Hi Karl,

I understand this is the R/qtl discussion page, but as you are an author for the R/qtlDesign package, I thought it would be OK to ask this on here.

I am in need of something like qtlDesign but for multiple founders do you know of a package that would be suitable. Even if there is one for GWAS in which I could include a pedigree that would also be useful.

Thanks,

Conor

Karl Broman

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Mar 14, 2022, 11:55:47 AM3/14/22

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Ian Mackay’s group has a recent paper in G3 about designing MAGIC populations; they have an R package and shiny app.

https://doi.org/10.1093/g3journal/jkab295

karl

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Conor Simpson

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Mar 14, 2022, 1:03:32 PM3/14/22

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Cheers Karl,

I have used this to describe my population and assess how well represented my founders are, in addition to how much recombination has been captured but I do not think I can use it to estimate the power of mapping a QTL of a given heritability using it. I will investigate a bit further as I am probably underutilized this tool.