get_coloc_results: Run coloc

In RHReynolds/colochelpR: `colochelpR` is a home for helper functions for executing coloc

Run coloc

Description

Wrapper function that joins the two formatted datasets and performs coloc analysis then annotates coloc results currently only allows for df1_type to be "quant" or "cc" and df2_type to be "quant" so if running GWAS vs eQTL, eQTL must be df2. Note: "quant" refers to a quantitative trait, while "cc" refers to "case-control".

Usage

get_coloc_results(
  df1,
  df2,
  harmonise = F,
  df1_type,
  df2_type,
  df1_beta_or_pval,
  df2_beta_or_pval,
  df1_N = NULL,
  df2_N = NULL,
  df_1_propor_cases,
  annotate_signif_SNP_df1_df2 = F,
  key_cols,
  df_1_name,
  df_2_name,
  df1_path,
  df2_path,
  p1 = 1e-04,
  p2 = 1e-04,
  p12 = 1e-05
)

Arguments

df1	df. First formatted dataset for coloc analysis.
df2	df. Second formatted dataset for coloc analysis.
harmonise	logical. Whether you would like to modify the sign of the beta so both datasets are with respect to the same allele
df1_type	Either "quant" or "cc".
df2_type	Only "quant" currently.
df1_beta_or_pval	Either "beta" or "pval" depending on whether you want to use betas or pvals in the coloc analysis
df2_beta_or_pval	Either "beta" or "pval" depending on whether you want to use betas or pvals in the coloc analysis
df1_N	num. Number of samples in df1 (only required for quant)
df2_N	num. Number of samples in df2 (only required for quant)
df_1_propor_cases	num. Option to put in the proportion of cases for a GWAS in coloc::coloc.abf().
annotate_signif_SNP_df1_df2	lgl. Whether to annotate results with the signif SNPs from df1/df2 and from coloc
key_cols	all columns needed to uniquely identify analysis - requires appending "_1" or "_2" depending on whether col from df1 or df2 respectively
df_1_name	chr. df1 name that will be added to results list (e.g. "GWAS")
df_2_name	chr. df2 name that will be added to results list (e.g. "eQTL")
df1_path	chr. Path to df1
df2_path	chr. Path to df2
p1	num. Prior probability a SNP is associated with trait 1, set to coloc.abf default of 1e-4
p2	num. Prior probability a SNP is associated with trait 2, set to coloc.abf default of 1e-4
p12	num. Prior probability a SNP is associated with both traits, set to coloc.abf default of 1e-5

Value

List containing coloc results annotated or NULL if there are no overlapping SNPs or all SNPs are removed through harmonisation

RHReynolds/colochelpR documentation built on June 18, 2022, 5:53 a.m.