runCancerTreatmentAnalysis: Execute the cancer characterization analysis

In cukarthik/CancerTreatmentCharacterization: What the package does (short line)

Description

Execute the cancer characterization analysis

Usage

runCancerTreatmentAnalysis(
  connection,
  cohortDatabaseSchema,
  cohortId,
  databaseId,
  outputFolder,
  minCellCount = 5
)

Arguments

connection	An object of type connection that has an established database connection.
cohortDatabaseSchema	Schema name where intermediate data can be stored. You will need to have write priviliges in this schema. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.
databaseId	A short string for identifying the database (e.g. 'Synpuf').
outputFolder	Name of local folder to place results; make sure to use forward slashes (/). Do not use a folder on a network drive since this greatly impacts performance.
minCellCount	The minimum number of subjects contributing to a count before it can be included in packaged results.
cdmDatabaseSchema	Schema name where your patient-level data in OMOP CDM format resides. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.
cohortTable	The name of the table that will be created in the work database schema. This table will hold the exposure and outcome cohorts used in this study.
oracleTempSchema	Should be used in Oracle to specify a schema where the user has write priviliges for storing temporary tables.
databaseName	The full name of the database (e.g. 'Medicare Claims Synthetic Public Use Files (SynPUFs)').
databaseDescription	A short description (several sentences) of the database.
createCohorts	Create the cohortTable table with the exposure and outcome cohorts?

Details

This function executes the cohort diagnostics.

cukarthik/CancerTreatmentCharacterization documentation built on Dec. 19, 2021, 7:03 p.m.