download.wide.format: Download in wide format the Labkey data for all or a selected...

In fitzgerald-lab/labkey.occams: Download and clean LabKey data

Download in wide format the Labkey data for all or a selected group of patients. NOTE: Major changes from 2020 Apr 22 onwards. All of the therapy tables are merged. There is no longer a TR.Chemotherapy column, to check if a patient has chemo look at TR.NeoAdj or TR.Adj columns. All followup/endpoint/recurrence tables are now merged. Only a single row per patient is provided with the most recent follow-up date, the date of recurrence (if there is one) and the date of death (if known).

Description

Download in wide format the Labkey data for all or a selected group of patients. NOTE: Major changes from 2020 Apr 22 onwards. All of the therapy tables are merged. There is no longer a TR.Chemotherapy column, to check if a patient has chemo look at TR.NeoAdj or TR.Adj columns. All followup/endpoint/recurrence tables are now merged. Only a single row per patient is provided with the most recent follow-up date, the date of recurrence (if there is one) and the date of death (if known).

Usage

download.wide.format(
  ocs,
  occams_ids = NULL,
  missing = NULL,
  versions = "z1",
  verbose = T
)

Arguments

ocs	Labkey connection object from connect.to.labkey()
occams_ids	Array of occams identifiers, this is optional. The default returns all patients, better to use get.patients(...) if you want this.
missing	Replace missing values with this string, default is NA
versions	The table versions used from labkey, default is 'z1'

Value

named list of tibbles: patients, family_history, tissues

Author(s)

skillcoyne

fitzgerald-lab/labkey.occams documentation built on June 12, 2022, 2:02 p.m.