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Layer bone GWAS

GWAS of the Lövstad 2015 layer experiment.

Update SNP chip markers to Galgal6

  • R/prepare_marker_fasta.R -- Read SNP chip design file and output source sequences for alignment.

  • scripts/markers_run_blat.sh -- Use Blat to align sequences to Galgal6

  • R/markers_filter_alignment.R -- Read output from Blat and make a map file with new positions.

Format plink files

  • R/make_pheno_table.R -- Collect all phenotypes in one file

  • R/prepare_plink_files.R -- Reads text files of genotypes and phenotypes to create ped and phenotype files

Exploratory analysis

  • R/plot_genotypes.R -- QC of SNP genotypes

  • R/plot_phenotypes.R -- Plots and linear models of bone strength and body weight

  • R/plot_pqct_tga_phenotypes.R -- Plots and linear models of pQCT and TGA phenotypes

  • R/trait_modelling_functions.R -- Helper functions

Run quantitative genetics and GWAS with hglm

  • scripts/convert_bed.sh -- Convert binary plink files for GEMMA

  • script/gemma_grm.sh -- Estimate GRM with GEMMA

  • R/hglm_gwas_prepare_data.R -- Set up data for main bone and body weight GWAS

  • R/hglm_gwas_prepare_data_crosses_separate.R -- Separate crossbred analysis

  • R/hglm_gwas_summary_crosses_separate.R -- Main analysis of GWAS of bone and body weight with separate crossbreds

  • R/hglm_gwas_summary_pqct_crosses_separate.R -- Main analysis of GWAS of QCT phenotypes with separate crossbreds

  • R/hglm_gwas.R -- Old joint GWAS analysis of bone and body weight

  • R/hglm_gwas_tga_prepare_data.R -- Set up data for QCT and TGA GWAS

  • R/hglm_gwas_tga.R -- QCT and TGA GWAS

  • R/hglm_models.R -- Quantitative genetics models with hglm

  • R/hglm_models_tga.R -- Quantitative genetics models for QCT and TGA

GWAS results

  • R/R/hglm_gwas_overlap_crosses_separate.R -- Summarise main GWAS results

  • R/hglm_gwas_summary.R -- Old joint GWAS analysis

  • R/hglm_gwas_summary_pqct_tga.R -- Summarise QCT and TGA GWAS

  • R/hglm_gwas_overlap.R -- Overlap GWAS results between traits

  • R/candidate_loci.R -- Look at candidate loci

Run GCTA for genomic correlations

  • R/genomic_correlation_prepare_files.R -- Prepare data for genomic correlation with GCTA

  • scripts/genomic_correlation_gcta.sh -- Run bivariate genomic model with GCTA

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