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diff --git a/topics/R-qtl2-format-notes.gmi b/topics/R-qtl2-format-notes.gmi new file mode 100644 index 0000000..705e065 --- /dev/null +++ b/topics/R-qtl2-format-notes.gmi @@ -0,0 +1,38 @@ +# 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). + +# References + +=> https://kbroman.org/qtl2/assets/vignettes/input_files.html +=> https://github.com/rqtl/qtl2data |