This function allows the user to create a cohort from the GENIE BPC data based on cancer diagnosis information such as cancer cohort, treating institution, histology, and stage at diagnosis, as well as cancer-directed regimen information including regimen name and regimen order. This function returns each of the clinical and genomic data files subset on the patients that met criteria for the analytic cohort. Documentation regarding the structure and contents of each file can be found in the Analytic Data Guide corresponding to each data release, as well as in the Clinical Data Structure vignette.
Usage
create_analytic_cohort(
data_synapse,
index_ca_seq = 1,
institution,
stage_dx,
histology,
regimen_drugs,
regimen_type = "Exact",
regimen_order,
regimen_order_type,
return_summary = FALSE
)Arguments
- data_synapse
The item from the nested list returned from pull_data_synapse() that corresponds to the cancer cohort of interest.
- index_ca_seq
Index cancer sequence. Default is 1, indicating the patient's first index cancer. The index cancer is also referred to as the BPC Project cancer in the GENIE BPC Analytic Data Guide; this is the cancer that met the eligibility criteria for the project and was selected at random for PRISSMM phenomic data curation. Specifying multiple index cancer sequences, e.g. index_ca_seq = c(1, 2) will return index cancers to patients with 1 index cancer and will return the first AND second index cancers to patients with multiple.
- institution
GENIE BPC participating institution. Must be one of "DFCI", "MSK", "UHN", or "VICC" for NSCLC, BLADDER, Prostate, and PANC cohorts; must be one of "DFCI", "MSK", "VICC" for CRC and BrCa. Default selection is all institutions. This parameter corresponds to the variable `institution` in the Analytic Data Guide.
- stage_dx
Stage at diagnosis. Must be one of "Stage I", "Stage II", "Stage III", "Stage I-III NOS", "Stage IV". The default selection is all stages. Note that if this parameter is specified, any cases that are missing stage information are automatically excluded from the resulting cohort. This parameter corresponds to the variable `stage_dx` in the Analytic Data Guide.
- histology
Cancer histology. For all cancer cohorts except for BrCa (breast cancer), this parameter corresponds to the variable `ca_hist_adeno_squamous` and must be one of "Adenocarcinoma", "Squamous cell", "Sarcoma", "Small cell carcinoma", "Carcinoma", "Other histologies/mixed tumor". For BrCa, this parameter corresponds to the variable `ca_hist_brca` and must be one of "Invasive lobular carcinoma", "Invasive ductal carcinoma", "Other histology". The default selection is all histologies. Note that if this parameter is specified, any cases that are missing histology information are automatically excluded from the resulting cohort.
- regimen_drugs
Vector with names of drugs in cancer-directed regimen, separated by a comma. For example, to specify a regimen consisting of Carboplatin and Pemetrexed, specify regimen_drugs = "Carboplatin, Pemetrexed". Acceptable values are found in the `drug_regimen_list` dataset provided with this package. This parameter corresponds to the variable `regimen_drugs` in the Analytic Data Guide.
- regimen_type
Indicates whether the regimen(s) specified in `regimen_drugs` indicates the exact regimen to return, or if regimens containing the drugs listed in `regimen_drugs` should be returned. Must be one of "Exact" or "Containing". The default is "Exact".
- regimen_order
Order of cancer-directed regimen. If multiple drugs are specified, `regimen_order` indicates the regimen order for all drugs; different values of `regimen_order` cannot be specified for different drug regimens. If multiple values are specified, e.g. c(1, 2), then drug regimens that met either order criteria are returned.
- regimen_order_type
Specifies whether the `regimen_order` parameter refers to the order of receipt of the drug regimen within the cancer diagnosis (across all other drug regimens; "within cancer") or the order of receipt of the drug regimen within the times that that drug regimen was administered (e.g. the first time carboplatin pemetrexed was received, out of all times that the patient received carboplatin pemetrexed; "within regimen"). Acceptable values are "within cancer" and "within regimen".
- return_summary
Specifies whether a summary table for the cohort is returned. Default is FALSE. The `gtsummary` package is required to return a summary table.
Value
A list of data frames containing clinical and next generation sequencing information for patients that met the specified criteria. Optionally, if return_summary = TRUE, the list also includes summary tables for the number of records per dataset (`tbl_overall_summary`) as well as tables of key cancer diagnosis (`tbl_cohort`), cancer-directed regimen (`tbl_drugs`) and next generation sequencing (`tbl_ngs`) variables.
Details
See the create_analytic_cohort vignette for further documentation and examples.
Examples
# Examples using package test data
# Example 1 ----------------------------------
# Create a cohort of all patients with stage IV NSCLC adenocarcinoma and
# obtain all of their corresponding clinical and genomic data
ex1 <- create_analytic_cohort(
data_synapse = genieBPC::nsclc_test_data,
stage_dx = "Stage IV",
histology = "Adenocarcinoma"
)
names(ex1)
#> [1] "cohort_pt_char" "cohort_ca_dx"
#> [3] "cohort_ca_dx_non_index" "cohort_ca_drugs"
#> [5] "cohort_prissmm_imaging" "cohort_prissmm_pathology"
#> [7] "cohort_prissmm_md" "cohort_ngs"
#> [9] "cohort_mutations_extended" "cohort_fusions"
#> [11] "cohort_cna"
# Example 2 ----------------------------------
# Create a cohort of all NSCLC patients who received Cisplatin,
# Pemetrexed Disodium or Cisplatin, Etoposide as their first drug regimen
# for their first index NSCLC
ex2 <- create_analytic_cohort(
data_synapse = genieBPC::nsclc_test_data,
regimen_drugs = c(
"Cisplatin, Pemetrexed Disodium",
"Cisplatin, Etoposide"
),
regimen_order = 1,
regimen_order_type = "within cancer"
)
# Example 3 ----------------------------------
# Create a cohort of all NSCLC patients who received Cisplatin, Pemetrexed
# Disodium at any time throughout the course of treatment for their
# cancer diagnosis,
# but in the event that the patient received the drug multiple times,
# only select the first time.
ex3 <- create_analytic_cohort(
data_synapse = genieBPC::nsclc_test_data,
regimen_drugs = c("Cisplatin, Pemetrexed Disodium"),
regimen_order = 1,
regimen_order_type = "within regimen"
)
# Example 4 ----------------------------------
# Using create_analytic_cohort with pull_data_synapse
set_synapse_credentials()
#> ✔ You are now connected to 'Synapse' with your Personal Access Token (`SYNAPSE_PAT`) for this R session!
#> NULL
nsclc_2_0 <- pull_data_synapse("NSCLC", version = "v2.0-public")
#> ✔ pt_char has been imported for "NSCLC_v2.0"
#> ✔ ca_dx_index has been imported for "NSCLC_v2.0"
#> ✔ ca_dx_non_index has been imported for "NSCLC_v2.0"
#> ✔ ca_drugs has been imported for "NSCLC_v2.0"
#> ✔ prissmm_imaging has been imported for "NSCLC_v2.0"
#> ✔ prissmm_pathology has been imported for "NSCLC_v2.0"
#> ✔ prissmm_md has been imported for "NSCLC_v2.0"
#> ✔ cpt has been imported for "NSCLC_v2.0"
#> ✔ mutations_extended has been imported for "NSCLC_v2.0"
#> ✔ fusions has been imported for "NSCLC_v2.0"
#> ✔ cna has been imported for "NSCLC_v2.0"
ex4 <- create_analytic_cohort(
data_synapse = nsclc_2_0$NSCLC_v2.0,
regimen_drugs = c("Cisplatin, Pemetrexed Disodium"),
regimen_order = 1,
regimen_order_type = "within regimen"
)