These are the files containing the input and output data of LIMIX for both gene-eQTLs (gene_) and 3ieQTLs (peak_). They are in HDF5 format, which is supported in Python and R (among many others): https://www.hdfgroup.org/HDF5/ The input files contain the following groups: - genotype: The genotype matrix (generated from the VCF file) and associated data, including: - genotype/col_header: Information about the columns (variants) in the genotype matrix - genotype/row_header: Information about the rows (lines/individuals) in the genotype matrix - NB: Each genotype is given as the number of copies of the minor allele (0, 1 or 2). Note that the minor allele is not always the same as the alternate allele, and is defined based only on the genotypes for the 80 lines provided in this file. - phenotype: The phenotype matrix, after normalisation, and associated data, including: - /phenotype/col_header: Information about the columns (one column per feature + developmental stage) - /phenotype/col_header/context: The developmental stage (2h/6h/10h) - /phenotype/col_header/gene_ID: ID of the feature (gene or 3i peak) - /phenotype/row_header: Information about the rows (lines/individuals) - /phenotype/geneIDallStages: List of feature IDs for which expression data is available in all three developmental stages (these were the features tested for eQTLs) - /phenotype/geneIDstage1: List of features IDs with data in the first (2h) developmental stage (and similarly for the other two) The output files contain one group per gene/3i end peak ID, with information about every variant that was tested for association with this feature. The information provided about each feature includes: - betaT: The estimate for the effect size coefficient beta - cis_chrom/pos: The chromosome and position of the variants tested - permPvalT: The empirical p-value after 10,000 permutations - thPvalT: The uncorrected, theoretical p-value Where T is either C for the common-effect test or S1..3 for the specific-effect tests in the first (2h), second (6h) or third (10h) stage.