Man pages for AndersenLab/cegwas
A set of functions to process phenotype data, perform GWAS, and perform post-mapping data processing for C. elegans.
| allele_distribution | Geographic distribution of alleles |
| calculate_VE | Calculate Variance Explained for Significant SNPs |
| cegwas_map | cegwas_map |
| fetch_id_type | Fetch Variant Type |
| find_peaks | Find Peaks from GWAS Peaks |
| fine_map_plot | Fine mapping plot of GWAS confidence interval |
| generate_kinship | Generate Kinship |
| generate_mapping | Generate Mapping variant set |
| gene_variants | Plot variants for gene |
| get_db | Get Database |
| get_vcf | Generate directory path to VCF file |
| gwas_mappings | GWAS Mappings |
| identify_CI | Identify confidence intervals associated with QTL. |
| interval_summary | Interval Summary |
| kinship | kinship |
| manplot | Manhattan Plot for GWAS Mapping Data |
| plot_peak_ld | Plot LD values for significant SNPs in a mapping |
| process_correlations | Combine Variant Correlation Data |
| process_mappings | Fully process GWAS mapping output |
| process_pheno | Process Phenotype Data |
| pxg_plot | PxG plot |
| qq_plot | QQ-plot implemented in ggplot2 |
| query_vcf | Query VCF Data |
| resolve_isotype | 'resolve_isotype' determines the isotype from a strain name. |
| snpeff | Browse Variant Info |
| snps | snps |
| spike | Spike in an effect for GWAS mapping |
| tajimas_d | Tajima's D |
| variant_correlation | Process QTL Intervals |
| vcf_to_matrix | VCF To Matrix |
