runDrugTarget_Annot_Bioassay: runDrugTarget_Annot_Bioassay

In girke-lab/drugTargetInteractions: Drug-Target Interactions

runDrugTarget_Annot_Bioassay

Description

Meta-function to obtain in one step both drug-target annotation and bioassay data.

Usage

runDrugTarget_Annot_Bioassay(res_list, up_col_id="ID", ens_gene_id,  cmpid_file=file.path(config$resultsPath,"cmp_ids.rds") ,config=genConfig(), ...) 

Arguments

res_list	Object obtained from getUniprotIDs function.
up_col_id	Column name in data.frames of res_list containing uniprot IDs, usually one of: 'ID', 'ID_up_sp' or 'ID_up_sp_tr'.
ens_gene_id	Named character vector with ENSEMBL gene IDs in name slot and gene symbols or other ID type in value slot
cmpid_file	Path to CMP ID mapping file, often named cmp_ids.rds.
config	General configuration. See genConfig.
...	Slot to pass on additional arguments.

Value

List with two components each containing a data.frame. The first one (Annotation) contains drug-target annotation data, and the second one (Bioassay) contains drug-target bioassay data.

Author(s)

Thomas Girke

References

References to be added...

See Also

See also: drugTargetAnnot and drugTargetBioactivity

Examples

	config = genConfig(chemblDbPath= 
									system.file("extdata", "chembl_sample.db", package="drugTargetInteractions"),
							  resultsPath = 
									system.file("extdata", "results", package="drugTargetInteractions"))

	## (1) Translate gene symbols to ENSEMBL gene IDs
	ensembl_gene_id <- c("ENSG00000001626", "ENSG00000168748")
	idMap <- getSymEnsUp(EnsDb="EnsDb.Hsapiens.v86", ids=ensembl_gene_id, idtype="ENSEMBL_GENE_ID")
	ens_gene_id <- idMap$ens_gene_id


	## (2a) Retrieve UniProt IDs with both IDMs and SSNN paralogs
	queryBy <- list(molType="gene", idType="ensembl_gene_id", ids=names(ens_gene_id))
	 
		#this function is slow and requires a network connection
		res_list <- getParalogs(queryBy)
	
	

	## (3) Obtain Drug-Target Annotation and Bioassay Data 
	drug_target_list <- runDrugTarget_Annot_Bioassay(res_list=res_list, 
											up_col_id="ID_up_sp", ens_gene_id,config=config ) 

girke-lab/drugTargetInteractions documentation built on Oct. 10, 2022, 10:35 p.m.