check_prostate_redcap: Quality Control Check for Prostate REDCap database

In stopsack/prostateredcap: Load and check the MSK Prostate REDCap Prostate clinical database

Quality Control Check for Prostate REDCap database

Description

Run sequential quality control checks and thereby restrict the pts and smp datasets to cases that pass certain criteria. trt (treatment) data are passed along without changes.

Usage

check_prostate_redcap(
  data,
  qc_crit_pts = qc_criteria_pts(),
  qc_crit_smp = qc_criteria_smp(),
  qc_level_pts = NULL,
  qc_level_smp = NULL,
  recommended_only = FALSE,
  time_origin = c("seq", "dx", "adt", "met")
)

Arguments

data	List with elements pts and smp, returned by load_prostate_redcap.
qc_crit_pts	Criteria for checking the pts tibble. Defaults to the return of the qc_criteria_pts function. Custom criteria can be supplied instead.
qc_crit_smp	Criteria for checking the smp tibble. Defaults to the return of the qc_criteria_smp function. Custom criteria can be supplied instead.
qc_level_pts	Level of QC that the return pts tibble will be restricted to. By default, all QC steps in qc_crit_pts will be applied. A integer index (row) number of qc_crit_pts can be provided instead to perform less strict exclusions. qc_level_pts = 1 will perform no exclusions.
qc_level_smp	As qc_level_pts, for smp.
recommended_only	Return qc'd pts and smp restricted to variables that are recommended for use in analyses? Defaults to FALSE but is recommended for use.
time_origin	Time origin for follow-up time scales: sequencing ("seq"), diagnosis ("dx"), from initiation of androgen deprivaiton therapy "adt", or from metastasis ("met")? Provide multiple origins as, e.g., c("dx", "seq"). Returns all variables by default or if recommended_only = FALSE.

Value

List:

• pts: Patient-level data after QC.

• smp: Sample-level data after QC.

• qc_pts: Tibble of sequential exclusions for pts.

• qc_smp: Tibble of sequential exclusions for smp. The qc_pts and qc_smp tibbles can be used to extract information on which records failed which QC step.

See Also

Overview of analysis-ready data elements: https://stopsack.github.io/prostateredcap/articles/dataelements.html

Examples

## Not run: 
# Process output of load_prostate_redcap():
pts_smp_qc <- check_prostate_redcap(pts_smp, recommended_only = TRUE)

## End(Not run)

stopsack/prostateredcap documentation built on June 3, 2023, 12:51 a.m.