selectSP_driver_byDB — selectSP_driver

selectSP_driver_byDB is used to select driver genes based on their interaction drug information, including predicted blood-brain barrier penetration and drug developing phase.

Usage

selectSP_driver_byDB(
  genes = NULL,
  select_type = NULL,
  database = NULL,
  select_phase = NULL
)

Arguments

genes: a character vector of genes for which the targeting drug phase or blood brain barrier penetration information are queried.
select_type: character, which drug information is required. User can choose from "BP_prediction" and "drug_phase".
database: character, which database will be used. "BPdb" contains drug blood brain barrier penetrantion information, others contain drug developing phase information. User can choose from "BPdb", "ChEMBL","Repurposing_HUB" and "Drugbank_V5.1".
select_phase: a character vector of drug phases will be used. For checking detailed phase information in each database, try to call helper functions: ChEMBL_drugphase_levels(); Repurposing_HUB_drugphase_levels(); Drugbank_drugphase_levels().

Examples

drugdb.preload()
#> Error in drugdb.preload(): could not find function "drugdb.preload"
genes<-c("MDM2","CDK4","CDK6","ATM","ATR","BCL2","BCL2L1","HDAC6","STAT3","JAK2")
sp_df<-selectSP_driver_byDB(genes=genes,select_type="BP_prediction",database="BPdb")
#> Error in selectSP_driver_byDB(genes = genes, select_type = "BP_prediction",     database = "BPdb"): could not find function "selectSP_driver_byDB"
sp_df<-selectSP_driver_byDB(genes=genes,select_type="drug_phase",database="Drugbank_V5.1")
#> Error in selectSP_driver_byDB(genes = genes, select_type = "drug_phase",     database = "Drugbank_V5.1"): could not find function "selectSP_driver_byDB"
sp_df<-selectSP_driver_byDB(genes=genes,select_type="drug_phase",database="Drugbank_V5.1",select_phase="approved")
#> Error in selectSP_driver_byDB(genes = genes, select_type = "drug_phase",     database = "Drugbank_V5.1", select_phase = "approved"): could not find function "selectSP_driver_byDB"
sp_df<-selectSP_driver_byDB(genes=genes,select_type="drug_phase",database="ChEMBL")
#> Error in selectSP_driver_byDB(genes = genes, select_type = "drug_phase",     database = "ChEMBL"): could not find function "selectSP_driver_byDB"
sp_df<-selectSP_driver_byDB(genes=genes,select_type="drug_phase",database="Repurposing_HUB")
#> Error in selectSP_driver_byDB(genes = genes, select_type = "drug_phase",     database = "Repurposing_HUB"): could not find function "selectSP_driver_byDB"
if (FALSE) { # \dontrun{
} # }