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_distributionGeographic distribution of alleles
calculate_VECalculate Variance Explained for Significant SNPs
fetch_id_typeFetch Variant Type
find_peaksFind Peaks from GWAS Peaks
fine_map_plotFine mapping plot of GWAS confidence interval
generate_kinshipGenerate Kinship
generate_mappingGenerate Mapping variant set
gene_variantsPlot variants for gene
get_dbGet Database
get_vcfGenerate directory path to VCF file
gwas_mappingsGWAS Mappings
identify_CIIdentify confidence intervals associated with QTL.
interval_summaryInterval Summary
manplotManhattan Plot for GWAS Mapping Data
plot_peak_ldPlot LD values for significant SNPs in a mapping
process_correlationsCombine Variant Correlation Data
process_mappingsFully process GWAS mapping output
process_phenoProcess Phenotype Data
pxg_plotPxG plot
qq_plotQQ-plot implemented in ggplot2
query_vcfQuery VCF Data
resolve_isotype'resolve_isotype' determines the isotype from a strain name.
snpeffBrowse Variant Info
spikeSpike in an effect for GWAS mapping
tajimas_dTajima's D
variant_correlationProcess QTL Intervals
vcf_to_matrixVCF To Matrix
AndersenLab/cegwas documentation built on May 5, 2019, 4:57 a.m.