getData: Get patient event and survival data from a database

In novasmedley/gbmSpm: Find predictive sequential patterns for clinical glioblastoma patients

Description

Get patient event and survival data from a database

getEventData: get event data from eventTable in database

getSurvData: get patient survival days and survival status from personTable in database

getDemographics: get patient demographics and two biomarkers from personTable in database

Usage

getData(database, eventTable, personTable)

getEventData(database, eventTable)

getSurvData(database, personTable)

getDemographics(database, personTable)

Arguments

database	a MySQL database, where connection is authenticated through a configuration file with group named database)
eventTable	an event-based table in database, containing at least: iois = patient id, char agent = event type, char agent_detail = event attribute, char startdate = event start datein the format 'YYYY-MM-DD', char enddate = event end date in the format 'YYYY-MM-DD', char recurrenceNum = patient's recurrence count (since baseline) during event, int daysSinceBaseline = days since baseline, int
personTable	a patient-based table in database, containing at least: iois = patient id, char survival = total survival days at time of data collection, int status = patient status at the end of data collection , 'DECEASED' or 'ALIVE', char DOB = date of birth in the format 'YYYY-MM-DD', char gender = gender, char ethnicity = ethnicity, char MSP = MGMT promoter methytation status, char ('U' = unmethylated, 'M' = methylated) IDH1 = status of IDH1 gene, char ('WT' = wild type, 'MUT' = mutated)

Details

Note: tumor lateriality and location is searched for in agent_detail regardless of agent/event type.

Value

getData returns a named list containing two dataframes, 'person' for patient data (returned by getSurvData) and 'event' for event data (returned by getEventData)

novasmedley/gbmSpm documentation built on May 17, 2019, 10:39 a.m.