## ----libraryLoad--------------------------------------------------------- suppressMessages(library(ENCODExplorer)) ## ---- eval=FALSE--------------------------------------------------------- # # the path (relative or absolute) to the future database # database_filename <- "new.encode.rda" # new_data <- export_ENCODEdb_matrix(database_filename, overwrite = FALSE) ## ----tables, eval=FALSE-------------------------------------------------- # # the path (relative or absolute) to the future database # database_filename = "new.encode.rda" # tables = prepare_ENCODEdb(database_filename) ## ----new_encode_df, eval = FALSE----------------------------------------- # new_encode_df <- export_ENCODEdb_matrix(tables) ## ----queryEncode, eval=FALSE--------------------------------------------- # query_results <- queryEncode(df = new_encode_df, assay = "switchgear", target ="elavl1", file_format = "bed" , fixed = F) # downloadEncode(df = new_encode_df, file_acc = query_results$file_accession)