BrapaNetworks

This repository contains code for building networks from B.rapa RIL RNAseq data described in Baker et al, 2019

I have taken two approaches: using mutual ranks and using WGCNA.

The main scripts are the .RMD files.

• 00_Annotation.Rmd blast to annotate B. rapa genes based on Arabidopsis homologs.
• 01_Process Counts.Rmd starts from RNAseq counts, normalizes and voom transforms in preparation for network building.
• 02_MR Clustering UN.Rmd Builds mutual rank networks centered on traits of interest
• 03_QTL_Annotation_MR_Genes.Rmd looks for overlaps between network genes and QTL
• 04_MR_eQTL_Overlap.Rmd maps eQTL for the MR genes and then looks for overlap between those eQTL and trait QTL
• 05_WGCNA_UN.Rmd build WGCNA networks
• 05b_WGCNA_UN_multi.Rmd testing different parameters on WGCNA. Also repeatability.
• 06_get_eigengene_QTL.Rmd maps QTL for the WGCNA eigen genes (cluster centers)
• 07_analyze_eigengene_QTL.Rmd
• 08_eigen_gene_module_correlation.Rmd Further examining eigen genes and modules
• 09_Bel1_SNPs.Rmd Look for SNPs in Bel1 gene
• 10_MR_SNPs.Rmd find SNPs in MR genes.