scanone Error "Following phenotypes are not numeric: Column"

[Jeevan Karloss]

Hello, 

When I run the following code, I get the below error. 

Code:

data.1D <- scanone(cross=data, chr=c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16"), pheno.col=c(2:85), model="np", use="complete.obs")

Error:

Error in checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata,  : 

  Following phenotypes are not numeric: Column

But when I read the same file using read.csv, that shows all the data in the file are numeric. 

May be its a simple novice question. 

Jeevan

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[Karl Broman]

At least one of the phenotype columns was interpreted as a factor rather than numeric.

If you try:

which(!sapply(data$pheno, is.numeric))

that should tell you which columns are not numeric, which might help.

For example:

data(hyper)
which(!sapply(hyper$pheno, is.numeric))

Note that it's best not to use 'data' as the name of your data, since that is an important R function.

If you send me your .csv data file (privately, to kbr...@biostat.wisc.edu), I could give you more detailed help.

karl

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