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# R/qtl2 Format Notes
This document is mostly to help other non-biologists figure out their way around the format(s) of the R/qtl2 files. It mostly deals with the meaning/significance of the various fields.
From the R/qtl2 format documentation:
> The comma-delimited (CSV) files are each in the form of a simple matrix, with the first column being a set of IDs and the first row being a set of variable names.
and
> All of these CSV files may be transposed relative to the form described below.
We are going to consider the "non-transposed" form here, for ease of documentation: simply flip the meanings as appropriate for the transposed files.
## geno files
> The genotype data file is a matrix of individuals × markers. The first column is the individual IDs; the first row is the marker names.
For GeneNetwork, this means that the first column contains the Sample names (previously "strain names"). The first row would be a list of markers.
## gmap and pmap files
The first column of the gmap/pmap file contains genetic marker values. There are no Individuals/samples (or strains) here.
## pheno files
The first column is the list of individuals (samples/strains) whereas the first column is the list of phenotypes.
## phenocovar files
These seem to contain extra metadata for the phenotypes.
The first column is the list of phenotype identifiers whereas the first column is a list of metadata headers (phenotype covariates).
As an example,
=> https://github.com/rqtl/qtl2data/blob/main/BXD/bxd_phenocovar.csv The phenocovar file for BXD mice
We see here that this contains the individual identifier (id), and a description for each individual/sample.
# References
=> https://kbroman.org/qtl2/assets/vignettes/input_files.html
=> https://github.com/rqtl/qtl2data
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