get.visit: Get Master Visit Data File with Proteomics

In pranavdorbala/proteomicsHF: ARIC Proteomics of Heart Failure -- Biomarker Discovery Pipeline

Description

This is the outward facing wrapper function to process and load data for analysis. This function will read SomaLogic and Study Data, Impute missing adjusting covariates, filter data for exclusions

Usage

get.visit(soma.data, path.mods, master)

Arguments

soma.data	SomaLogic Proteomic Raw Data from get.soma()
path.mods	Char vector path to folder structure containing new adjustment variables, filtering conditions, and outcome variables. This folder must contain csv files formatted as detailed in get.adjust(). This function expects that adjustment variables will be in adjusted.csv, outcome variables in outcomes.csv and filters in filters.csv.
master	Tibble of master data file with study data. Output of haven::read_dta() function.

Value

Tibble of study data merged with Proteomics Data, labelled, and filtered.

Examples

## Not run: 
labels <- get.labels('data/proteinMapping.csv', sid,
                     uniprot.full.name,
                     entrezgenesymbol,
                     flag2 == 0)
aric.master <- haven::read_dta('data/ARICmaster_121820.dta')
soma.data <- get.soma('data/somaV5.txt', labels)

fifth.visit <- get.visit(soma.data = soma.data,
                         path.mods = 'data/visit-five',
                         labels = labels,
                         master = aric.master))

## End(Not run)

pranavdorbala/proteomicsHF documentation built on March 9, 2021, 12:22 a.m.