reconcile_data: Combine and reconcile the three main data components needed...

In tbilab/meToolkit: Build and Customize Phewas Multimorbidity Explorer Apps.

Description

Helper function used at the begining of a ME app that takes the raw format of the three data sets required, phewas results, individual snp copies, and individual phenotype pairs, and combines them into a list object that combines individual data and checks phewas results along with extracting the snp name from the column of the genotype file.

Usage

reconcile_data(
  phewas_results,
  id_to_snp,
  id_to_code,
  multiple_comparisons_adjustment
)

Arguments

phewas_results	Dataframe containing the results of the phewas study. Needs columns p_val, id, category(along with accompanying color), tooltip.
id_to_snp	Dataframe containing columns on id, snp(# copies of allele).
id_to_code	Dataframe containing column id, and columns for each code included.
multiple_comparisons_adjustment	What type of multiple comparisons adjustment should be done to the phewas results? Options include "None", "Bonferroni", and "Benjamini-Hochberg". Note that the correction is performed before filtering of codes to those contained in individual data. Aka for as many tests as were passed in raw phewas results. If different behavior is desired, the user must provide results pre-adjusted.

Value

List with snp_name, individual_data, and phewas_results properties for use in ME app.

Examples

reconcile_data(phewas_table, id_to_snp, phenotype_id_pairs)

tbilab/meToolkit documentation built on June 23, 2020, 9:55 a.m.