Converting file to R/qtl2 format

[Eric Heinze]

Dear R/qtl users,

I am attempting to perform a QTL analysis from a VCF file.  Currently, I have created two CSV files using suggestions from a previous thread.  One file is an SNP matrix with marker genotypes, and the other has marker name, chromosome, and position.  

Is there an easy way to make these files into one that is acceptable for the R/qtl2 package?  I am very new to QTL and would appreciate any help in this regard.

Thanks,

Eric

[Karl Broman]

I’m not sure about “easy”. 

The input file format is described at https://kbroman.org/qtl2/assets/vignettes/input_files.html

There are sample data files at https://kbroman.org/qtl2/pages/sampledata.html

as well as at https://github.com/rqtl/qtl2data

The latter includes, in many cases, R scripts to prepare the data files.

For example, see https://github.com/rqtl/qtl2data/blob/main/BXD/R/convertData.R

karl