readInputFile: Convert input data to OMOP formated data via CDM and mask

In AndrewC160/ROMOPOmics: ROMOPOmics: incorporating 'Omics Data Into The Observational Medical Outcomes Partnership (OMOP) Data Model

Description

readInputFile() takes a TSV/CSV file containing an input data set to be converted to the common data model format, that dataset's mask as formatted by loadModelMask(), and the desired data model produced by loadDataModel(). This function reads in that data table and funnels its fields into the appropriate tables and fields for the data model. All data tables are included at this stage, including those with no entries, which allows any data set produced by this function to be incorporated into the same database as long as the same data model was used. As such, the output tables are "exhaustive" in that no unused columns are dropped.

Usage

readInputFile(
  input_file,
  data_model,
  mask_table,
  transpose_input_table = FALSE
)

Arguments

input_file	Name of a TSV/CSV file containing required alias column names.
data_model	Data model being used, typically as a tibble returned by loadDataModel().
mask_table	Mask contained in a tibble, typically as a tibble loaded by loadModelMask().
transpose_input_table	Boolean; defaults to FALSE. If TRUE, transpose tables with one row per treatment/sample to one per column. readInputFile()

AndrewC160/ROMOPOmics documentation built on Jan. 27, 2021, 6:57 p.m.