README.txt

Additional File 4 - QTL mapping data and scripts

The file QTL_mapping.org contains a complete set of R scripts for the
QTL analysis of family 4 of the JAMA x PAXB cross and the fine mapping
analysis on chromosome 4 using individuals from multiple families. The
file is best viewed in Emacs org-mode but can be opened in any text
editor. There is also a QTL_mapping.html file, which contains the same
code and is formatted for viewing in the browser.

Data files
  fam4.geno.csv           Genotypes of Family 4 fish used for QTL mapping
  fam4.geno.initial.csv   Genotype data before initial cleanup and processing
  fam4.pheno.csv          Phenotype data for family 4 (spine lengths, standard
                                                       length, body depth, sex)
  fine_mapping_genotypes.csv   Genotypes from 7 F2 families for 48 markers in
                               chromosome 4 region of interest, coded as A,B,H
			       for marine, freshwater, and heterozygous
  fine_mapping_phenotypes.csv  Spine measurements for the larger set up F2 fish


Other files are generated or referenced explicitly in the scripts