## ----libraryLoad---------------------------------------------------------
suppressMessages(library(ENCODExplorer))

## ---- eval=FALSE---------------------------------------------------------
#  # the path (relative or absolute) to the future database
#  database_filename <- "new.encode.sqlite"
#  new_data <- update_ENCODExplorer(database_filename, overwrite = FALSE)

## ----tables, eval=FALSE--------------------------------------------------
#  # the path (relative or absolute) to the future database
#  database_filename = "new.encode.sqlite"
#  tables = prepare_ENCODEdb(database_filename)

## ----new_encode_df, eval = FALSE-----------------------------------------
#  new_encode_df <- export_ENCODEdb_matrix(database_filename)

## ----new_accession_df, eval = FALSE--------------------------------------
#  new_accession_df <- export_ENCODEdb_accession(new_encode_df, database_filename)

## ----queryEncode, eval=FALSE---------------------------------------------
#  query_results <- queryEncode(df = new_encode_df, assay = "switchgear", target ="elavl1", file_format = "bed_broadPeak" , fixed = F)
#  downloadEncode(df = new_encode_df, resultSet = query_results, resultOrigin = "queryEncode")