## ----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)