subset_to_codes: Subset phenotype data to a given list of phecodes

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

Description

Removes individuals who have none of the requested codes

Usage

subset_to_codes(data, desired_codes, codes_to_invert = c())

Arguments

data	A wide phenotype file with columns IID, snp, and all the normalized phecode names
desired_codes	Character vector of the phecodes to be extracted
codes_to_invert	Character vector of phecodes that the user has requested be inverted (e.g. not having the code is considered 'having' it.)

Value

A wide dataframe with just the columns desired and only rows corresponding to cases with one or more of the desired codes.

Examples

subset_to_codes(myPhenotypes, c('001.00', '002.00'), codes_to_invert = c('001.00'))

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