Error in convert_sex...

[Jennifer Jacob]

I am running a 'dof1' association and am getting the following error:

Error in convert_sex(control$sex, output$covar, control$sep, control$comment.char,  : 

  sex column "sex" not found in covar

Here is my control file script and the first few rows of the .csv file with the 'sex' column. 

All the mice are female. Is that a problem? If not, what am I missing? TIA!

[Dan Gatti]

Usually, this means that some file doesn’t have sample IDs aligned. I find that if my genotypes were ever a data.frame and if R changed the column names, that cryptic errors like this show up.

 

Dan

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[Karl Broman]

I think include

covar_file=“dof1_covar.csv”,

crossinfo_covar=“ngen”

and delete the lines with crossinfo_file and crossinfo_codes

karl

[Jennifer Jacob]

Thank you Dan. I'll take a look at that.

[Jennifer Jacob]

Karl, I tried that and get this error instead; which was what led me to the code I posted previously.

Error in convert_cross_info(control$cross_info, output$covar, control$sep,  :
  1 missing values in cross_info (cross_info can't be missing).

[Karl Broman]

There is apparently a missing value somewhere in that ngen column. Find it and either fix it or remove that line.

karl

[Jennifer Jacob]

If I run the 'control_file' script as you indicated but designate the 'crosstype' as "do" rather than "dof1", it runs without errors.

On Monday, May 13, 2024 at 12:55:10 PM UTC-4 Karl Broman wrote:

[Jennifer Jacob]

Nevermind my last message, I'll remove the line.

[Jennifer Jacob]

I have an FVB in there, so that is where the issue probably lies. 

As a non-DO, what is the best way to indicate "ngen"?