RImmPort_Article.R
In RImmPort: RImmPort: Enabling Ready-for-analysis Immunology Research Data

## ----eval=FALSE---------------------------------------------------------------
#  
#  # Truncated code to improve clarity - for illustration purpose only
#  
#  Study <- setRefClass("Study", fields = list(
#    special_purpose="SpecialPurpose",
#    interventions="Interventions",
#    events="Events",
#    findings="Findings",
#    trial_design="TrialDesign"),
#    ...
#  ))
#  
#  SpecialPurpose <- setRefClass("SpecialPurpose",
#                               fields = list(
#                                 dm_l="list",
#                                 sv_l="list"),
#                               ...
#  
#  Interventions <- setRefClass("Interventions",
#                                  fields = list(
#                                    cm_l="list",
#                                    ex_l="list",
#                                    su_l="list"),
#                               ...
#  
#  Events <- setRefClass("Events", fields = list(
#                                    ae_l="list",
#                                    dv_l="list",
#                                    mh_l="list",
#                                    apmh_l="list"),
#                        ...
#  
#  Findings <- setRefClass("Findings",
#                          fields = list(
#                                  lb_l="list",
#                                  pe_l="list",
#                                  vs_l="list",
#                                  qs_l="list",
#                                  fa_l="list",
#                                  sr_l="list",
#                                  pf_l="list",
#                                  za_l="list",
#                                  zb_l="list",
#                                  zc_l="list",
#                                  zd_l="list"),
#                          ...
#  
#  TrialDesign <- setRefClass("TrialDesign",
#                          fields = list(
#                            ta_l="list",
#                            ti_l="list",
#                            ts_l="list"),
#                          ...
#  
#  

## -----------------------------------------------------------------------------
library(RImmPort)
library(DBI)
library(sqldf)
library(plyr)

## ----eval=FALSE---------------------------------------------------------------
#  
#  # provide appropriate MySQL database connection parameters
#  mysql_conn <- dbConnect(MySQL(), user="username", password="password",
#                     dbname="database",host="host")
#  
#  # set the data source as the ImmPort MySQL database.
#  

## ----eval=FALSE---------------------------------------------------------------
#  setImmPortDataSource(mysql_conn)

## ----eval=FALSE---------------------------------------------------------------
#  # get the directory where ImmPort sample data is stored in the directory structure of RImmPort package
#  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")
#  list.files(tab_dir)

## ----eval=FALSE---------------------------------------------------------------
#  # set db_dir to the folder where the database file 'ImmPort.sqlite' should be stored
#  db_dir <- file.path(studies_dir, "Db")

## ----eval=FALSE---------------------------------------------------------------
#  # build a new ImmPort SQLite database with the data in the downloaded zip files
#  buildNewSqliteDb(tab_dir, db_dir)

## ----eval=FALSE---------------------------------------------------------------
#  list.files(db_dir)

## -----------------------------------------------------------------------------
# get the directory of a sample SQLite database that has been bundled into the RImmPort package
db_dir <- system.file("extdata", "ImmPortStudies", "Db", package = "RImmPort")

# connect to the database
sqlite_conn <- dbConnect(SQLite(), dbname=file.path(db_dir, "ImmPort.sqlite"))

# set the ImmPort SQLite database as the ImmPort data source
setImmPortDataSource(sqlite_conn)

## -----------------------------------------------------------------------------
# view documentation on Study
?Study

# get all study ids
getListOfStudies()

# load the entire data of study: `SDY139`
study_id <- 'SDY139'
sdy139 <- getStudy(study_id)

# access Demographics data of SDY139
dm_df <- sdy139$special_purpose$dm_l$dm_df
head(dm_df)

# access Concomitant Medications data of SDY139
cm_df <- sdy139$interventions$cm_l$cm_df
head(cm_df)

# get Trial Title from Trial Summary
ts_df <- sdy139$trial_design$ts_l$ts_df
title <- ts_df$TSVAL[ts_df$TSPARMCD== "TITLE"]
title

## -----------------------------------------------------------------------------

# get the list of names of all supported Domains
getListOfDomains()

?"Demographics Domain"

# get domain code of Demographics domain
domain_name <- "Demographics"
getDomainCode(domain_name)

dm_l <- getDomainDataOfStudies(domain_name, "SDY139")
if (length(dm_l) > 0) 
  names(dm_l)
head(dm_l$dm_df)


## -----------------------------------------------------------------------------
# get list of studies with Cellular Quantification data
domain_name <- "Cellular Quantification"
study_ids_l <- getStudiesWithSpecificDomainData(domain_name)
study_ids_l

## -----------------------------------------------------------------------------
# get Cellular Quantification data of studies `SDY139` and `SDY208`

# get domain code of Cellular Quantification domain
domain_name <- "Cellular Quantification"
getDomainCode(domain_name)

study_ids <- c("SDY139", "SDY208")
domain_name <- "Cellular Quantification"
zb_l <- getDomainDataOfStudies(domain_name, study_ids)
if (length(zb_l) > 0) 
  names(zb_l)
head(zb_l$zb_df)

## -----------------------------------------------------------------------------
getListOfAssayTypes()

## -----------------------------------------------------------------------------

# get 'ELISPOT' data of study `SDY139`
assay_type <- "ELISPOT"
study_id = "SDY139"
elispot_l <- getAssayDataOfStudies(study_id, assay_type)
if (length(elispot_l) > 0)
  names(elispot_l)
head(elispot_l$zb_df)


## ----eval=FALSE---------------------------------------------------------------
#  # get the directory where ImmPort sample data is stored in the directory structure of RImmPort package
#  studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")
#  
#  # serialize all of the data of studies `SDY139` and `SDY208'
#  study_ids <- c('SDY139', 'SDY208')
#  
#  # the folder where the .rds files will be stored
#  rds_dir <- file.path(studies_dir, "Rds")
#  
#  serialzeStudyData(study_ids, rds_dir)
#  list.files(rds_dir)
#  

## -----------------------------------------------------------------------------
# get the directory where ImmPort sample data is stored in the directory structure of RImmPort package
studies_dir <- system.file("extdata", "ImmPortStudies", package = "RImmPort")

# the folder where the .rds files will be stored
rds_dir <- file.path(studies_dir, "Rds")

# list the studies that have been serialized
list.files(rds_dir)

# load the serialized data of study `SDY208` 
study_id <- 'SDY208'
dm_l <- loadSerializedStudyData(rds_dir, study_id, "Demographics")
head(dm_l[[1]])


## -----------------------------------------------------------------------------
# get the directory where ImmPort sample data is stored in the directory structure of RImmPort package
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")
list.files(tab_dir)

# set db_dir to the folder where the database file 'ImmPort.sqlite' should be stored
db_dir <- file.path(studies_dir, "Db")

## ----eval=FALSE---------------------------------------------------------------
#  # build a new ImmPort SQLite database with the data in the downloaded zip files
#  buildNewSqliteDb(tab_dir, db_dir)

## -----------------------------------------------------------------------------
list.files(db_dir)