Package 'RImmPort'

Title: RImmPort: Enabling Ready-for-analysis Immunology Research Data
Description: The RImmPort package simplifies access to ImmPort data for analysis in the R environment. It provides a standards-based interface to the ImmPort study data that is in a proprietary format.
Authors: Ravi Shankar <[email protected]>
Maintainer: Zicheng Hu <[email protected]>, Ravi Shankar <[email protected]>
License: GPL-3
Version: 1.35.0
Built: 2024-10-31 04:23:48 UTC
Source: https://github.com/bioc/RImmPort

Help Index

Adverse Events Domain

Description

The Adverse Events data of an ImmPort study is reformated to the CDISC SDTM Adverse Events (AE) domain model, and is a list of 2 data frames containing 1) Adverse Events data AE and 2) any supplemental Adverse Events data SUPP

Adverse Events Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
AESEQ Sequence Number
AESPID Sponsor-Defined Identifier
AETERM Reported Term for the Adverse Event
AEMODIFY Modified Reported Term
AEBODYSYS Body System or Organ Class
AELOC Location of Event
AESEV Severity/Intensity
AEACN Action Taken with Study Treatment
AEACNOTH Other Action Taken
AEREL Causality
AERELNST Relationship to Non-Study Treatment
AEOUT Outcome of Adverse Event
AESTDY Study Day of Start of Adverse Event
AEENDY Study Day of End of Adverse Event

Associated Persons Medical History Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
APID Associated Persons Identifier
MHSEQ Sequence Number
RSUBJID Related Subject
SREL Subject Relationship
MHTERM Reported Term for the Medical History
MHCAT Category for Medical History
MHBODSYS Body System or Organ Class
MHDTC Date/Time of History Collection
MHDY RStudy Day of History Collection

Associated Persons Medical History Domain

Description

The Associated Persons Medical History data of an ImmPort study is reformated to the CDISC SDTM AAssociated Persons Medical History (APMH) domain model, and is a list of 2 data frames containing 1) Associated Persons Medical History data APMH and 2) any supplemental Associated Persons Medical History data SUPP

buildNewSqliteDb

Description

The function buildSqliteDb builds a sqlite db of ImmPort study data. It takes in as input the study files in the TSV (Tab) format.

Usage

buildNewSqliteDb(data_dir, db_dir)

Arguments

data_dir

File directory where the study TSV files are stored
db_dir

File directory where the sqlite database will be stored

Value

The SQLite database name

Examples

studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
# set tab_dir to the folder where the zip files are located
tab_dir <- file.path(studies_dir, "Tab")
# set db_dir to the folder where the database file 'ImmPort.sqlite' should be stored
db_dir <- file.path(studies_dir, "Db")
# build a new ImmPort SQLite database with the data in the downloaded zip files
# dbname <- buildNewSqliteDb(tab_dir, db_dir)

Cellular Quantification Domain

Description

The ImmPort study data generated from assays of types: Flow and ELISPOT are grouped into the Cellular Quantification Domain. The data is reformated to a custom Cellular Quantification domain model in CDISC SDTM standards, and is a list of 2 data frames containing 1) Cellular Quantification data ZB and 2) any supplemental Cellular Quantification data SUPP

Concomitant Medications Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
CMSEQ Sequence Number
CMTRT Reported Name of Drug, Med, or Therapy
CMCAT Category for Medication
CMDOSE Dose per Administration
CMDOSTXT Dose Description
CMDOSU Dose Units
CMDOSFREQ Dosing Frequency per Interval
CMROUTE Route of Administration
CMSTDTC Start Date/Time of Medication
CMENDTC End Date/Time of Medication
CMSTDY Study Day of Start of Medication
CMENDY Study Day of End of Medication

Concomitant Medications Domain

Description

The Concomitant Medications data of an ImmPort study is reformated to the CDISC SDTM Concomitant Medications (CM) domain model, and is a list of 2 data frames containing 1) Concomitant Medications data CM and 2) any supplemental Concomitant Medications data SUPP

Demographics Domain

Description

The Demographics data of an ImmPort study is reformated to the CDISC SDTM Demographics (DM) domain model, and is a list of 2 data frames containing 1) Demographics data DM and 2) any supplemental Demographics data SUPP

Demographics Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
AGE Age
AGEU Age Units
SEX Sex
RACE Race (only for human data)
ETHNIC Ethnicity (only for human data)
SPECIES Species (only for non-human data)
STRAIN Strain/Substrain (only for non-human data)
SBSTRAIN Strain/Substrain Details (only for non-human data)
ARMCD Planned Arm Code
ARM Description of Planned Arm

Protocol Deviations Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
DVSEQ Sequence Number
DVTERM Protocol Deviation Term

Events class

Description

Events class

Fields

ae_l

Adverse Events data AE and supplemental Adverse Events data SUPP

dv_l

Protocol Deviations data DV and supplemental Protocol Deviations data SUPPDV

mh_l

Medical History data MH and supplemental Medical History data SUPPMH

apmh_l

Associated Persons Medical History data APMH and supplemental Associated Persons Medical History data SUPP

Examples

library(DBI)
library(sqldf)
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
db_dir <- file.path(studies_dir, "Db")
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))
setImmPortDataSource(sqlite_conn)
sdy139 <- getStudy("SDY139")
ae_df <- sdy139$events$ae_l$ae_df

Exposure Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
EXSEQ Sequence Number
EXTRT Name of Treatment
EXCAT Category of Treatment
EXDOSE Dose
EXDOSTXT Dose Description
EXDOSU Dose Units
EXDOSFRQ Dosing Frequency per Interval
EXROUTE Route of Administration
EXSTDTC Start Date/Time of Treatment
EXENDTC End Date/Time of Treatment
EXSTDY Study Day of Start of Treatment
EXENDY Study Day of End of Treatment

Exposure Domain

Description

The Exposure data of an ImmPort study is reformated to the CDISC SDTM Exposure (EX) domain model, and is a list of 2 data frames containing 1) Exposure data EX and 2) any supplemental Exposure data SUPP

Findings About Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
FASEQ Sequence Number
FATEST Findings About Test Name
FAOBJ Object of the Observation
FACAT Category for Findings About
FAORRES Results or Findings in Original Units
FAORRESU Original Units
FALOC Location of the Finding About
VISITNUM Visit Number
VISIT Visit Name
FADY Study Day of Collection

Findings About Domain

Description

The Findings About data of an ImmPort study is reformated to the CDISC SDTM Findings About (FA) domain model, and is a list of 2 data frames containing 1) Findings About data FA and 2) any supplemental Findings About data SUPPFA

Findings class

Description

Findings class

Fields

lb_l

Laboratory Test Results data LB and supplemental Laboratory Test Results data SUPPLB

pe_l

Physical Examination data PE and supplemental Physical Examination data SUPPPE

vs_l

Vital Signs data VS and supplemental Vital Signs data SUPPVS

qs_l

Questionnaires data QS and supplemental Questionnaires data SUPP

fa_l

Findings About data FA and supplemental Findings About data SUPPFA

sr_l

Skin Response data SR and supplemental Skin Response data SUPP

pf_l

Genetics Findings data PF and supplemental Genetics Findings data SUPPPF

za_l

Protein Quantification data ZA and supplemental Protein Quantification data SUPPZA

zb_l

Cellular Quantification data ZB and supplemental Cellular Quantification data SUPP

zc_l

Nucleic Acid Quantification data ZC and supplemental Nucleic Acid Quantification data SUPP

zd_l

Titer Assay Results data ZD and supplemental Titer Assay Results data SUPP

Examples

library(DBI)
library(sqldf)
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
db_dir <- file.path(studies_dir, "Db")
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))
setImmPortDataSource(sqlite_conn)
sdy139 <- getStudy("SDY139")
zb_df <- sdy139$findings$zb_l$zb_df

Genetics Findings Domain

Description

The ImmPort study data generated from assays of types: HLA Typing and Array are grouped into the Genetics Findings Domain. The data is reformated to a PharmacoGenomics and Genetics Findings (PF) model in CDISC SDTM standards, and is a list of 2 data frames containing 1) Genetics Findings data PF and 2) any supplemental Genetics Findings data SUPP

Get specific assay data of one or more studies from the ImmPort database

Description

Get specific assay data of one or more studies from the ImmPort database

Usage

getAssayDataOfStudies(study_ids, assay_type)

Arguments

study_ids

List of study indentifiers
assay_type

Assay Type

Value

a list of 1) domain data of specicifc assay technology and 2) any supplemental domain data of the studies

Author(s)

Ravi Shankar

Examples

library(DBI)
library(sqldf)
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
db_dir <- file.path(studies_dir, "Db")
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))
setImmPortDataSource(sqlite_conn)
elispot_l <- getAssayDataOfStudies("SDY139", "ELISPOT")
if (length(elispot_l) > 0)
  names(elispot_l)
head(elispot_l$zb_df)

Get code of a specific domain

Description

The function getListOfDomains returns the code of a specific domain

Usage

getDomainCode(domain)

Arguments

domain

Name of a specific domain

Value

A list of of all domain names and codes

Examples

domain <- "Demographics"
 code <- getDomainCode(domain)

Get specific domain data of one or more studies from the ImmPort database

Description

Get specific domain data of one or more studies from the ImmPort database

Usage

getDomainDataOfStudies(domain, study_ids)

Arguments

domain

Name of a specific domain
study_ids

List of study indentifiers

Value

a list of 1) domain data and 2) supplemental domain data of the studies

Examples

library(DBI)
library(sqldf)
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
db_dir <- file.path(studies_dir, "Db")
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))
setImmPortDataSource(sqlite_conn)
dm_df <- getDomainDataOfStudies("Demographics", "SDY139")

Get a list of Assay Types

Description

The function getListOfAssayTypes returns a list of assay types that ImmPort studies have employed in their experimetal assays

Usage

getListOfAssayTypes()

Value

A list of assay types

Examples

at_l <- getListOfAssayTypes()

Get names of all domains and their codes

Description

The function getListOfDomains returns a list of all domain names and codes

Usage

getListOfDomains()

Value

A list of of all domain names and codes

Examples

domains_df <- getListOfDomains()

Get a list of all studies

Description

Get a list of all studies

Usage

getListOfStudies()

Value

List of study indentifiers

Examples

library(DBI)
library(sqldf)
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
db_dir <- file.path(studies_dir, "Db")
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))
setImmPortDataSource(sqlite_conn)
study_ids <- getListOfStudies()

Get a list of studies that have specific assay type data

Description

Get a list of studies that have specific assay type data

Usage

getStudiesWithSpecificAssayData(assay_type, all_study_ids = c("ALL"))

Arguments

assay_type

Assay Type
all_study_ids

List of study indentifiers to search on

Value

List of study indentifiers

Examples

library(DBI)
library(sqldf)
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
db_dir <- file.path(studies_dir, "Db")
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))
setImmPortDataSource(sqlite_conn)
study_ids <- getStudiesWithSpecificAssayData("ELISPOT")

Get a list of studies that have specific domain data

Description

Get a list of studies that have specific domain data

Usage

getStudiesWithSpecificDomainData(domain, all_study_ids = c("ALL"))

Arguments

domain

Name of a specific domain
all_study_ids

List of study indentifiers to search on

Value

List of study indentifiers

Examples

library(DBI)
library(sqldf)
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
db_dir <- file.path(studies_dir, "Db")
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))
setImmPortDataSource(sqlite_conn)
study_ids <- getStudiesWithSpecificDomainData("Demographics")

Get all data of a specific study from the ImmPort data source

Description

The function getStudy queries the ImmPort data source for data of a specific study in all domains. The data is then structured into Study as classes, domains, variables and values.

Usage

getStudy(study_id)

Arguments

study_id

Identifier of a specific study

Value

A study data object where in all data are structured as classes, domains, variables and values (in CDISC format)

Examples

library(DBI)
library(sqldf)
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
db_dir <- file.path(studies_dir, "Db")
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))
setImmPortDataSource(sqlite_conn)
sdy139 <- getStudy("SDY139")

Interventions class

Description

Interventions class

Fields

cm_l

Concomitant Medications data CM and supplemental Concomitant Medications data SUPP

ex_l

Exposure data EX and supplemental Exposure data SUPP

su_l

Substance Use data SU and supplemental Substance Use data SUPP

Examples

library(DBI)
library(sqldf)
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
db_dir <- file.path(studies_dir, "Db")
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))
setImmPortDataSource(sqlite_conn)
sdy139 <- getStudy("SDY139")
cm_df <- sdy139$interventions$cm_l$cm_df

Laboratory Test Results Domain

Description

The Laboratory Test Results data of an ImmPort study is reformated to the CDISC SDTM Laboratory Test Results (LB) domain model, and is a list of 2 data frames containing 1) Laboratory Test Results data LB and 2) any supplemental Laboratory Test Results data SUPPLB

Laboratory Test Results Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
LBSEQ Sequence Number
LBTEST Lab Test or Examination Name
LBCAT Category for Lab Test
LBORRES Result or Finding in Original Units
LBORRESU Original Units
LBSPEC Specimen Type
LBREFID Specimen Identifier
VISITNUM Visit Number
VISIT Visit Name
LBELTM Planned Elapsed Time from Time Point Ref
LBTPTREF Time Point Reference

Load the Serialized Data of a Study

Description

Load the serialzed data (.rds) file of a specific domain of a study study from the directory where the file is located

Usage

loadSerializedStudyData(data_dir, study_id, domain)

Arguments

data_dir

Path to a file folder where the .rds study files reside
study_id

Study indentifier
domain

Domain of interest

Value

A study data object where in all data are structured as classes, domains, variables and values (in CDISC format)

Examples

studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
# the folder where the .rds files will be stored
rds_dir <- file.path(studies_dir, "Rds")
# load the serialized data of study `SDY208` 
loadSerializedStudyData(rds_dir, 'SDY208', "Demographics")

Medical History Domain

Description

The Medical History data of an ImmPort study is reformated to the CDISC SDTM Medical History (MH) domain model, and is a list of 2 data frames containing 1) Medical History data MH and 2) any supplemental Medical History data SUPPMH

Merge the Domain dataframe and Supplemental dataframe (long form)

Description

The Domain data list comprises of the the Domain datafrome that is in wide form, and any Supplemental dataframe that is in long form. The function mergeDomainAndSupplemental transposes the Supplemental dataframe into a wide form, and merges it with the Domain dataframe.

Usage

mergeDomainAndSupplemental(data_list)

Arguments

data_list

A list of 1) Domain dataframe and 2) any Supplemental dataframe

Value

The merged dataframe

Examples

library(DBI)
library(sqldf)
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
db_dir <- file.path(studies_dir, "Db")
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))
setImmPortDataSource(sqlite_conn)
l <- getDomainDataOfStudies("Cellular Quantification", "SDY208")
df <- mergeDomainAndSupplemental(l)

Medical History Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
MHSEQ Sequence Number
MHTERM Reported Term for the Medical History
MHCAT Category for Medical History
MHBODSYS Body System or Organ Class
MHDY Study Day of History Collection

Nucleic Acid Quantification Domain

Description

The ImmPort study data generated from assays of types: PCR are grouped into the Nucleic Acid Quantification Domain. The data is reformated to a custom Nucleic Acid Quantification domain model in CDISC SDTM standards, and is a list of 2 data frames containing 1) Nucleic Acid Quantification data ZC and 2) any supplemental Nucleic Acid Quantification data SUPP

Physical Examination Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
PESEQ Sequence Number
PETEST Body System Examined
PECAT Category for Examination
PEBODSYS Body System or Organ Class
PEORRES Verbatim Examination Finding
PEORRESU Original Units
PELOC Location of Physical Exam Finding
VISITNUM Visit Number
VISIT Visit Name
PEDY Study Day of Examination

Genetics Findings Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
PFSEQ Sequence Number
PFGRPID Group Identifier
PFTEST Test Name
PFCAT Category for Test
PFMETHOD Method of the Test
PFGENRI Genetic Region of Interest
PFORRES Result or Finding in Original Units
PFALLELC Allele (Chromosome) Identifier
PFSPEC Specimen Type
PFREFID Reference ID (Specimen Identifier)
VISITNUM Visit Number
VISIT Visit Name
PFELTM Planned Elapsed Time from Time Point Ref
PFTPTREF Time Point Reference
PFXFN Raw Data File or Life Science Identifier

Physical Examination Domain

Description

The Physical Examination data of an ImmPort study is reformated to the CDISC SDTM Physical Examination (PE) domain model, and is a list of 2 data frames containing 1) Physical Examination data PE and 2) any supplemental Physical Examination data SUPPPE

Protein Quantification Domain

Description

The ImmPort study data generated from assays of types: ELISA and MBAA are grouped into the Cellular Quantification Domain. The data is reformated to a custom Protein Quantification domain model in CDISC SDTM standards, and is a list of 2 data frames containing 1) Protein Quantification data ZA and 2) any supplemental Protein Quantification data SUPP

Protocol Deviations Domain

Description

The Protocol Deviations data of an ImmPort study is reformated to the CDISC SDTM Protocol Deviations (DV) domain model, and is a list of 2 data frames containing 1) Protocol Deviations data DV and 2) any supplemental Protocol Deviations data SUPPDV

Questionnaires Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
QSSEQ Sequence Number
QSTEST Questionnaires Test Name
QSCAT Category for Questionnaires
QSORRES Results or Findings in Original Units
QSORRESU Original Units
VISITNUM Visit Number
VISIT Visit Name
QSDY Study Day of Finding

Questionnaires Domain

Description

The Questionnaires data of an ImmPort study is reformated to the CDISC SDTM Questionnaires (QS) domain model, and is a list of 2 data frames containing 1) Questionnaires data QS and 2) any supplemental Questionnaires data SUPP

RImmPort: Enabling ready-for-analysis immunology research data

Description

The 'RImmPort' package simplifies access to ImmPort data for analysis, as the name implies, in the R statistical environment. It provides a standards-based interface to the ImmPort study data that is in a proprietary format.

Serialize the Study Data

Description

Load specific studies from the database and save it in .rds format in a local file directory

Usage

serialzeStudyData(study_ids, data_dir)

Arguments

study_ids

List of study indentifiers
data_dir

Path to a file folder where the .rds study files will be saved into

Value

List of study indentifiers that were serialized successfully

Examples

library(DBI)
library(sqldf)
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
db_dir <- file.path(studies_dir, "Db")
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))
setImmPortDataSource(sqlite_conn)
# the folder where the .rds files will be stored
rds_dir <- file.path(studies_dir, "Rds")
study_ids <- c('SDY139', 'SDY208')
serialzeStudyData(study_ids, rds_dir)

Set ImmPort data ource

Description

The function setImmPortDataSource sets the data source variable in RImmPort environment, to the connection handle to the MySQL or SQLite database, or to the file directory where the pre-created RImmPort-formatted files are stored.

Usage

setImmPortDataSource(data_src)

Arguments

data_src

A connection handle to ImmPort (MySQL or SQLite) database instance or a directory handle to folder where study RImmPort-formatted (.rds) files located

Value

1 if successful

Examples

library(DBI)
library(sqldf)
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
db_dir <- file.path(studies_dir, "Db")
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))
setImmPortDataSource(sqlite_conn)

Skin Response Domain

Description

The Skin Response data of an ImmPort study is reformated to the CDISC SDTM Skin Response (SR) domain model, and is a list of 2 data frames containing 1) Skin Response data SR and 2) any supplemental Skin Response data SUPP

Special Purpose class

Description

Special Purpose class

Fields

dm_l

Demographics data DM and supplemental Demographics data SUPP

Examples

library(DBI)
library(sqldf)
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
db_dir <- file.path(studies_dir, "Db")
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))
setImmPortDataSource(sqlite_conn)
sdy139 <- getStudy("SDY139")
dm_df <- sdy139$special_purpose$dm_l$dm_df

Skin Response Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
SRSEQ Sequence Number
SRTEST Skin Response Test or Examination Name
SROBJ Object of the Observation
SRCAT Category for Test
SRORRES Results or Findings in Original Units
SRORRESU Original Units
SRLOC Location used for Measurement
VISITNUM Visit Number
VISIT Visit Name
SRDY Study Day of Visit/Collection/Exam

Study class

Description

Study class

Fields

special_purpose

SpecialPurpose

interventions

Interventions

events

Events

findings

Findings

trial_design

TrialDesign

Examples

library(DBI)
library(sqldf)
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
db_dir <- file.path(studies_dir, "Db")
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))
setImmPortDataSource(sqlite_conn)
sdy139 <- getStudy("SDY139")

Substance Use Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
SUSEQ Sequence Number
SUTRT Reported Name of Substance
SUCAT Category of Substance Use
SUDOSE Substance Use Consumption
SUDOSTXT Substance Use Consumption Text
SUDOSU Consumption Units
SUDOSFRQ Use Frequency per Interval
SUROUTE Route of Administration
SUSTDTC Start Date/Time of Substance Use
SUENDTC End Date/Time of Substance Use
SUSTDY Study Day of Start of Substance Use
SUENDY Study Day of End of Substance Use

Subject Visits Domain

Description

Actual subject visits data of an ImmPort study is reformated to the CDISC SDTM Subject Visits (SV) domain model, and is a list of 2 data frames containing 1) Subject Visits data SV and 2) any supplemental Subject Visits data SUPP

Substance Use Domain

Description

The Substance Use data of an ImmPort study is reformated to the CDISC SDTM Substance Use (SU) domain model, and is a list of 2 data frames containing 1) Substance Use data SU and 2) any supplemental Substance Use data SUPP

Supplemental Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
RDOMAIN Related Domain Abbreviation
USUBJID Unique Subject Identifier
IDVAR Identifying Variable
IDVARVAL Identifying Variable Value
QNAM Qualifier Variable Name
QLABEL Qualifier Variable Label
QVAL Data Value

Protocol Deviations Domain Supplemental Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
RDOMAIN Related Domain Abbreviation
USUBJID Unique Subject Identifier
IDVAR Identifying Variable
IDVARVAL Identifying Variable Value
QNAM Qualifier Variable Name
QLABEL Qualifier Variable Label
QVAL Data Value

Note

The following table enumerates the values in QNAM and QLABEL variables

QNAM QLABEL
DVRELAE Is Deviation Related to an Adverse Event?
DVREASON Reason for Deviation
DVRESOL Resulotion of Deviation
DVCONT Did Subject continued in Study?
DVSTDY Study Day of Start of Deviation
DVENDY Study Day of End of Deviation

Findings About Domain Supplemental Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
RDOMAIN Related Domain Abbreviation
USUBJID Unique Subject Identifier
FASEQ Sequence Number
IDVAR Identifying Variable
IDVARVAL Identifying Variable Value
QNAM Qualifier Variable Name
QLABEL Qualifier Variable Label
QVAL Data Value

Note

The following table enumerates the values in QNAM and QLABEL variables

QNAM QLABEL
FATOD Time of Day of Collection

Laboratory Test Results Domain Supplemental Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
RDOMAIN Related Domain Abbreviation
USUBJID Unique Subject Identifier
IDVAR Identifying Variable
IDVARVAL Identifying Variable Value
QNAM Qualifier Variable Name
QLABEL Qualifier Variable Label
QVAL Data Value

Note

The following table enumerates the values in QNAM and QLABEL variables

QNAM QLABEL
LBSPECSB Specimen Subtype
VISITMIN Planned Visit Minimum Start Day
VISITMAX Planned Visit Maximum Start Day

Medical History Domain Supplemental Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
RDOMAIN Related Domain Abbreviation
USUBJID Unique Subject Identifier
MHSEQ Sequence Number
IDVAR Identifying Variable
IDVARVAL Identifying Variable Value
QNAM Qualifier Variable Name
QLABEL Qualifier Variable Label
QVAL Data Value

Note

The following table enumerates the values in QNAM and QLABEL variables

QNAM QLABEL
MHAGE Age at Onset
MHAGEU Age at Onset Units
MHTOD Time of Day

Physical Examination Domain Supplemental Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
RDOMAIN Related Domain Abbreviation
USUBJID Unique Subject Identifier
PESEQ Sequence Number
IDVAR Identifying Variable
IDVARVAL Identifying Variable Value
QNAM Qualifier Variable Name
QLABEL Qualifier Variable Label
QVAL Data Value

Note

The following table enumerates the values in QNAM and QLABEL variables

QNAM QLABEL
PETOD Time of Day

Genetics Findings Domain Supplemental Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
RDOMAIN Related Domain Abbreviation
USUBJID Unique Subject Identifier
IDVAR Identifying Variable
IDVARVAL Identifying Variable Value
QNAM Qualifier Variable Name
QLABEL Qualifier Variable Label
QVAL Data Value

Note

The following table enumerates the values in QNAM and QLABEL variables

QNAM QLABEL
PFPOPAR Geographic Area of the Population
PFSPECSB Specimen Subtype
PFREFIDP Source Specimen Identifier
VISITMIN Planned Visit Minimum Start Day
VISITMAX Planned Visit Maximum Start Day
PFSPTRT Specimen Treatment
PFTRTAMV Specimen Treatment Amount Value
PFTRTAMU Specimen Treatment Amount Unit
PFTRTDUV Specimen Treatment Duration Value
PFTRTDUU Specimen Treatment Duration Unit
PFTRTTMV Specimen Treatment Temperature Value
PFTRTTMU Specimen Treatment Temperature Unit

Vital Signs Domain Supplemental Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
RDOMAIN Related Domain Abbreviation
USUBJID Unique Subject Identifier
VSSEQ Sequence Number
IDVAR Identifying Variable
IDVARVAL Identifying Variable Value
QNAM Qualifier Variable Name
QLABEL Qualifier Variable Label
QVAL Data Value

Note

The following table enumerates the values in QNAM and QLABEL variables

QNAM QLABEL
VSTOD Time of Day

Protein Quantification Domain Supplemental Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
RDOMAIN Related Domain Abbreviation
USUBJID Unique Subject Identifier
IDVAR Identifying Variable
IDVARVAL Identifying Variable Value
QNAM Qualifier Variable Name
QLABEL Qualifier Variable Label
QVAL Data Value

Note

The following table enumerates the values in QNAM and QLABEL variables

QNAM QLABEL
ZAMFI MFI
ZAMFICRD MFI Coordinate
ZASPECSB Specimen Subtype
ZAREFIDP Source Specimen Identifier
VISITMIN Planned Visit Minimum Start Day
VISITMAX Planned Visit Maximum Start Day
ZASPTRT Specimen Treatment
ZATRTAMV Specimen Treatment Amount Value
ZATRTAMU Specimen Treatment Amount Unit
ZATRTDUV Specimen Treatment Duration Value
ZATRTDUU Specimen Treatment Duration Unit
ZATRTTMV Specimen Treatment Temperature Value
ZATRTTMU Specimen Treatment Temperature Unit

Cellular Quantification Domain Supplemental Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
RDOMAIN Related Domain Abbreviation
USUBJID Unique Subject Identifier
IDVAR Identifying Variable
IDVARVAL Identifying Variable Value
QNAM Qualifier Variable Name
QLABEL Qualifier Variable Label
QVAL Data Value

Note

The following table enumerates the values in QNAM and QLABEL variables

QNAM QLABEL
ZBSPECSB Specimen Subtype
ZBREFIDP Source Specimen Identifier
ZBFCF Control Files Names
VISITMIN Planned Visit Minimum Start Day
VISITMAX Planned Visit Maximum Start Day
ZBSPTRT Specimen Treatment
ZBTRTAMV Specimen Treatment Amount Value
ZBTRTAMU Specimen Treatment Amount Unit
ZBTRTDUV Specimen Treatment Duration Value
ZBTRTDUU Specimen Treatment Duration Unit
ZBTRTTMV Specimen Treatment Temperature Value
ZBTRTTMU Specimen Treatment Temperature Unit

Nucleic Acid Quantification Domain Supplemental Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
RDOMAIN Related Domain Abbreviation
USUBJID Unique Subject Identifier
IDVAR Identifying Variable
IDVARVAL Identifying Variable Value
QNAM Qualifier Variable Name
QLABEL Qualifier Variable Label
QVAL Data Value

Note

The following table enumerates the values in QNAM and QLABEL variables

QNAM QLABEL
ZCSPECSB Specimen Subtype
ZCREFIDP Source Specimen Identifier
VISITMIN Planned Visit Minimum Start Day
VISITMAX Planned Visit Maximum Start Day
ZCSPTRT Specimen Treatment
ZCTRTAMV Specimen Treatment Amount Value
ZCTRTAMU Specimen Treatment Amount Unit
ZCTRTDUV Specimen Treatment Duration Value
ZCTRTDUU Specimen Treatment Duration Unit
ZCTRTTMV Specimen Treatment Temperature Value
ZCTRTTMU Specimen Treatment Temperature Unit

Titer Assay Results Domain Supplemental Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
RDOMAIN Related Domain Abbreviation
USUBJID Unique Subject Identifier
IDVAR Identifying Variable
IDVARVAL Identifying Variable Value
QNAM Qualifier Variable Name
QLABEL Qualifier Variable Label
QVAL Data Value

Note

The following table enumerates the values in QNAM and QLABEL variables

QNAM QLABEL
ZDSPECSB Specimen Subtype
ZDREFIDP Source Specimen Identifier
VISITMIN Planned Visit Minimum Start Day
VISITMAX Planned Visit Maximum Start Day
ZDSPTRT Specimen Treatment
ZDTRTAMV Specimen Treatment Amount Value
ZDTRTAMU Specimen Treatment Amount Unit
ZDTRTDUV Specimen Treatment Duration Value
ZDTRTDUU Specimen Treatment Duration Unit
ZDTRTTMV Specimen Treatment Temperature Value
ZDTRTTMU Specimen Treatment Temperature Unit

Subject Visits Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
VISITNUM Visit Number
VISIT Visit Name
SVSTDY Study Day of Start of Visit

Trial Arms Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
ARMCD Planned Arm Code
ARM Name of Planned Arm
ARMDESC Description of Planned Arm
ARMRULE Population Selection Rule

Trial Inclusion Exclusion Criteria Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
IETEST Inclusion/Exclusion Criterion
IECAT Inclusion/Exclusion Category

Titer Assay Results Domain

Description

The ImmPort study data generated from assays of types: HAI and Neut Ab Titer are grouped into the Titer Assay Results Domain. The data is reformated to a custom Titer Assay Results domain model in CDISC SDTM standards, and is a list of 2 data frames containing 1) Titer Assay Results data ZD and 2) any supplemental Titer Assay Results data SUPP

Trial Arms Domain

Description

The Trial Arms data of an ImmPort study is reformated to the CDISC SDTM Trial Arms (TA) domain model, and is a list of 2 data frames containing 1) Trial Arms data TA and 2) any supplemental Trial Arms data SUPP

Trial Inclusion Exclusion Criteria Domain

Description

The Trial Inclusion Exclusion Criteria data of an ImmPort study is reformated to the CDISC SDTM Trial Inclusion Exclusion Criteria (TI) domain model, and is a list of 2 data frames containing 1) Trial Inclusion Exclusion Criteria data TI and 2) any supplemental Trial Inclusion Exclusion Criteria data SUPP

Trial Summary Domain

Description

The Trial Summary data of an ImmPort study is reformated to the CDISC SDTM Trial Summary (TS) domain model, and is a list of 2 data frames containing 1) Trial Summary data TS and 2) any supplemental Trial Summary data SUPP

Trial Visits Domain

Description

Information on the planned visits of an ImmPort study is reformated to the CDISC SDTM Trial Visits (TV) domain model, and is a list of 2 data frames containing 1) Trial Visits data TV and 2) any supplemental Trial Visits data SUPP

Trial Design class

Description

Trial Design class

Fields

ta_l

Trial Arms data TA and supplemental Trial Arms data SUPP

tv_l

Trial Visits data TA and supplemental Trial Visits data SUPP

ti_l

Trial Inclusion Exclusion Criteria data TI and supplemental Trial Inclusion Exclusion Criteria data SUPP

ts_l

Trial Summary data TS and supplemental Trial Summary data SUPP

Examples

library(DBI)
library(sqldf)
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
db_dir <- file.path(studies_dir, "Db")
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))
setImmPortDataSource(sqlite_conn)
sdy139 <- getStudy("SDY139")
ts_df <- sdy139$trial_design$ts_l$ts_df

Trial Summary Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
TSSEQ Sequence Number
TSPARMCD Trial Summary Parameter Short Name
TSPARM Trial Summary Parameter
TSVAL Parameter Value

Note

The following table enumerates the values in TSPARMCD and TSPARM variables

TSPARMCD TSPARM
TITLE Trial Title
DESCR Trial Description
INDIC Trial Indication
TRT Investigational Therapy or Treatment
HYPOTHS Trial Hypotheses
SSTDTC Study Start Date
SENDTC Study End Date
PLANSUB Planned Number of Subjects
ACTSUB Actual Number of Subjects
AGEMAX Planned Maximum Age of Subjects
AGEMIN Planned Minimum Age of Subjects
AGEU Age Units
SEXPOP Sex of Participants
SPONSOR Clinical Study Sponsor
PUBRLDAT Public Release Date
ISTRIAL Study Type
RESFOCUS Trial Research Focus

Trial Visits Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
VISITNUM Visit Number
VISIT Visit Name
ARMCD Planned Arm Code
ARM Name of Planned Arm
TVSTRL Visit Start Rule
TVENRL Visit End Rule

Vital Signs Domain

Description

The Vital Signs data of an ImmPort study is reformated to the CDISC SDTM Vital Signs (VS) domain model, and is a list of 2 data frames containing 1) Vital Signs data VS and 2) any supplemental Vital Signs data SUPPVS

Vital Signs Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
VSSEQ Sequence Number
VSTEST Vital Signs Test Name
VSCAT Category for Vital Signs
VSORRES Result or Finding in Original Units
VSORRESU Original Units
VSLOC Location of Vital Signs Measurement
VISITNUM Visit Number
VISIT Visit Name
VSDY Study Day of Vital Signs

Protein Quantification Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
ZASEQ Sequence Number
ZATEST Protein Quantification Test Name
ZACAT Category for Protein Quantification
ZAMETHOD Measurement Technique
ZAANALYT Analyte
ZAORRES Result or Finding in Original Units
ZAORRESU Original Units
ZASPEC Specimen Type
VISITNUM Visit Number
VISIT Visit Name
ZAELTM Planned Elapsed Time from Time Point Ref
ZATPTREF Time Point Reference
ZAREFID Specimen Identifier
ZAXFN Raw Data File or Life Science Identifier

Cellular Quantification Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
ZBSEQ Sequence Number
ZBTEST Cellular Quantification Test Name
ZBCAT Category for Cellular Quantification
ZBMETHOD Measurement Technique
ZBPOPDEF Cell Population Definition
ZBPOPNAM Cell Population Name
ZBORRES Result or Finding in Original Units
ZBORRESU Original Units
ZBBASPOP Base Parent Population
ZBSPEC Specimen Type
VISITNUM Visit Number
VISIT Visit Name
ZBELTM Planned Elapsed Time from Time Point Ref
ZBTPTREF Time Point Reference
ZBREFID Specimen Identifier
ZBXFN Raw Data File or Life Science Identifier

Nucleic Acid Quantification Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
ZCSEQ Sequence Number
ZCTEST Nucleic Acid Quantification Test Name
ZCCAT Category for Nucleic Acid Quantification
ZCMETHOD Measurement Technique
ZCENTRZD Entrez Gene ID
ZCGENNAM Gene Name
ZCGENSYM Gene Symbol
ZCORRES Result or Finding in Original Units
ZCORRESU Original Units
ZCSPEC Specimen Type
ZCREFID Specimen Identifier
VISITNUM Visit Number
VISIT Visit Name
ZCELTM Planned Elapsed Time from Time Point Ref
ZCTPTREF Time Point Reference

Titer Assay Results Domain Variables

Description

Variable Name Variable Label
STUDYID Study Identifier
DOMAIN Domain Abbreviation
USUBJID Unique Subject Identifier
ZDSEQ Sequence Number
ZDTEST Titer Assay Results Test Name
ZDCAT Category for Titer Assay Results
ZDMETHOD Measurement Technique
ZDSTRAIN Virus Strain
ZDORRES Result or Finding in Original Units
ZDORRESU Original Units
ZDSPEC Specimen Type
ZDREFID Specimen Identifier
VISITNUM Visit Number
VISIT Visit Name
ZDELTM Planned Elapsed Time from Time Point Ref
ZDTPTREF Time Point Reference
ZDXFN Raw Data File or Life Science Identifier