Skip to content

Latest commit

 

History

History
23 lines (16 loc) · 1.16 KB

README.md

File metadata and controls

23 lines (16 loc) · 1.16 KB
Raw

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.