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Fetch Protein-protein interaction for given gene IDs from Hit Predict database

Source: R/searchHP.R
searchHP.Rd

This function searches the Hitpredict database to retrieve the Experimental Protein-Protein Interaction data.

Usage

searchHP(
  geneID,
  taxid = "36329",
  uniprotToGID = TRUE,
  timeout = 60,
  max_tries = 3
)

Arguments

geneID

Single gene ID.

taxid

Taxon ID of the organism of interest. Default: 36329. If taxon id of organism is not known set this to NULL.

uniprotToGID

To convert Uniprot ID to gene ID. Set TRUE for Plasmodium geneIDs only.

timeout

Seconds after which timeout must be considered.

max_tries

Maximum retries to access the database.

Value

A data frame, containing 11 columns: "Interaction", "Interactor", "Name", "Experiments", "Category", "Method.Score", "Annotation.Score", "Interaction.Score", "Confidence", "QueryID", "ensembl_gene_id".

Examples

if (FALSE) { # \dontrun{
test <- searchHP("Q8I1Q4")

## To use it for other organism, turn off uniprotToGID and provide taxid of the organism
test <- searchHP("BRCA1",taxid = "9606" , uniprotToGID = FALSE)
} # }