process_mappings: Fully process GWAS mapping output

In AndersenLab/cegwas: A set of functions to process phenotype data, perform GWAS, and perform post-mapping data processing for C. elegans.

Description

process_mappings takes gwas_mappings output and calculates variance explained and identifies peaks and associated confidence intervals

Usage

process_mappings(mapping_df, phenotype_df, CI_size = 50, snp_grouping = 200,
  BF = NA)

Arguments

mapping_df	Output from gwas_mappings function
phenotype_df	phenotype data frame generated by process_pheno. two element list. element 1 : traits. element 2: trait values with strains in columns with each row corresponding to trait in element 1
CI_size	defines the size (in # SNPs) of confidence intervals. Default is 50 and is defined in more detail below.
snp_grouping	defines grouping of peaks. Defined further below, default is 200.
BF	defines a custom bonferroni correction.

Details

This function combines calculate_VE, find_peaks, and identify_CI into one function when intermediate dataframes are not wanted

Value

Outputs processed mapping dataframe that contains original mapping dataframe with appended information for significant SNPs only, including: variance explained, confidence interval information, genotype information

AndersenLab/cegwas documentation built on March 6, 2020, 1:10 a.m.