CIM with multiple phenotypes

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Nathaniel Burner

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Mar 5, 2024, 6:42:31 PMMar 5

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Hi Karl,

I am trying to run a CIM on multiple independent phenotypes by specifying a vector of pheno columns with:

> qtl.cim = cim(qtl, pheno.col = 3:14, n.marcovar = 2, window = 5, + method = "imp", error.prob = 0.0001, map.function = "kosambi") Error in markerforwself2(g, y, n.marcovar) : Need length(y) == nrow(x).

however, I get the error after. Specifying a vector of pheno columns worked just fine for the scanone command. Is a CIM with multiple phenotypes possible?

Thanks

Karl Broman

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Mar 7, 2024, 8:45:39 AMMar 7

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The cim() function can take only a single phenotype column at a time. You can specify it with either a column number or column name.

Sorry; I’ll try to revise the help information to clarify this, and revise the function to give a better error message.