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.
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.
The first column of the gmap/pmap file contains genetic marker values. There are no Individuals/samples (or strains) here.
The first column is the list of individuals (samples/strains) whereas the first column is the list of phenotypes.
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,
We see here that this contains the individual identifier (id), and a description for each individual/sample.