#This archive contains scripts and data files to duplicate all analyses in the accompanying paper. To run, open the file README.R in R, and follow the included instructions. # Of particular interest is the script labeled "Run_quantitative_genetics_models_MCMC.R". This scripts implements the hierarchical Bayesian mixed-effect modelwe describe to robustly estimate genetic parameters from the gene expression data. #This file links to subscripts that perform individual analyses from the paper: # Genetics of gene expression responses to temperature stress in a sea urchin gene network # Daniel E Runcie, David A Garfield, Courtney C Babbitt, Jennifer A Wygoda, Sayan Mukherjee, Gregory A Wray #all scripts run in R 2.13.1 #Instructions: download all files from Dryad into the same working directory. Then run the following scripts. The order of the four data sets is not important #necessary libraries library(Biobase) library(gdata) library(xtable) library(edgeR) library(MCMCpack) library(mnormt) library(beanplot) #morphological analysis #Data files: # morphology_data.dat: raw morphology data source("Analyze_morphology.R", print.eval =T) #qPCR analysis #Data files: # qPCR_Ct_scores.dat: raw qPCR data source("qPCR_analysis.R", print.eval =T) #RNA-seq analysis #Data files: folder RNA_seq_data # geneInfo.dat: gene annotation information # sample_info.txt: sample annotation information for RNA-seq samples # GLEAN-3.1.gff3-chado-UTR_onlyExon_removedDuplicates_lessRedundant: gff3 format file defining locations of exons for each gene model on Spurp genome v3.1 # SPU_counts.txt: RNA-seq data file. Counts of reads in each gene model defined by above GFF file in each sample # RNAseq_results.txt: concentrations and log2FC estimates due to temperature for each gene in RNAseq analysis source("RNA_seq_analysis.R",print.eval=T) #Gene network analysis #Data files: folder DASL_data # DASL_featureData.dat: annotation data for features on DASL array # DASL_phenoData.dat: annotation data for samples analyzed by DASL # DASL_varMetadata.dat: blank file necessary for processing # raw_DASL_intensities_G_channel.dat: Raw (bead-summarized) DASL data for all samples in the green (Cy3) channel # raw_DASL_intensities_R_channel.dat: Raw (bead-summarized) DASL data for all samples in the red (Cy5) channel # Network_gene_annotation.dat: annotation information for the genes analyzed by DASL # Network_interactions_list.dat: description of the interactions known from the endomesoderm and ectoderm gene regulatory networks. source("Pre_process_DASL_data.R") source("Run_quantitative_genetics_models_MCMC.R",print.eval=T) source("Gene_network_analysis.R",print.eval=T)