diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..5ca0973 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +.DS_Store + diff --git a/data/mock/bgdc2021.csv b/data/mock/bgdc2021.csv new file mode 100644 index 0000000..db55c82 --- /dev/null +++ b/data/mock/bgdc2021.csv @@ -0,0 +1,7 @@ +individual,generic +generic,blood +sample_type,blood +seq,RNASeq +sample,sample00 +gene,ABCB1 +variant,rs12345 \ No newline at end of file diff --git a/data/mock/bgdc2021_mask.csv b/data/mock/bgdc2021_mask.csv new file mode 100644 index 0000000..0bc7b62 --- /dev/null +++ b/data/mock/bgdc2021_mask.csv @@ -0,0 +1,7 @@ +alias,example1,field,table,field_idx,set_value +individual,meep,person_source_value,person,NA,NA +sample_type,blood,anatomic_site_source_value,specimen,NA,NA +seq,RNASeq,sequencing_source_value,sequencing,NA,NA +sample,GSM,specimen_source_value,specimen,NA,NA +gene,ARID1A,gene_source_value,gene,1,NA +variant,rs,variant_source_value,variation,1,NA \ No newline at end of file diff --git a/src/R/mock_romopomics_example.R b/src/R/mock_romopomics_example.R new file mode 100644 index 0000000..c8d9cd0 --- /dev/null +++ b/src/R/mock_romopomics_example.R @@ -0,0 +1,24 @@ +pacman::p_load(tidyverse) + +#install.packages("devtools") +devtools::install_github("ngiangre/ROMOPOmics",force=T) + +library(ROMOPOmics) + +dm_file <- + system.file("extdata","OMOP_CDM_v6_0_custom.csv",package="ROMOPOmics",mustWork = TRUE) +dm <- + loadDataModel(master_table_file = dm_file) + +omop_inputs <- + list( + bgdc2021= + readInputFile( + input_file = "data/mock/bgdc2021.csv", + data_model = dm, + mask_table = loadModelMasks("data/mock/bgdc2021_mask.csv") + ) + ) +db_inputs <- combineInputTables(input_table_list = omop_inputs) +omop_db <- buildSQLDBR(omop_tables = db_inputs,file.path(tempdir(),"mock.sqlite")) +DBI::dbListTables(omop_db)