process_mappings: Fully process GWAS mapping output

Description Usage Arguments Details Value

View source: R/process_mappings.R

Description

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

Usage

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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.