Conditional QTL mapping

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Shikha

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Mar 10, 2022, 9:37:27 AM3/10/22

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Dear Dr. Broman,

Is there a way to calculate conditional trait values followed by conditional QTL mapping in R/qtl?

Specifically, I want to see the effect of Trait 1 conditional on another Trait 2 (T1|T2), so that the phenotypic values of Trait 1 are the net trait values which are independent of variation in Trait 2. This is to understand the genetic basis (pleiotropy/tight linkage) of colocalised QTL for Trait 1 and Trait 2.

Any comments, thoughts or suggestions would be greatly appreciated.

Thanks,

Shikha

Karl Broman

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Mar 10, 2022, 9:39:11 AM3/10/22

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This is not included in R/qtl. But you could use the R function lm() to fit the regression of trait 1 on trait 2, and the residuals.