HPiP: Host-Pathogen Interaction Prediction

    #' Gold-standard Reference Set of Inter-Species PPIs
    #' @description This dataset consists of experimentally validated
    #' human-SARS-CoV-2 interactions (positive set) and
    #' non-interacting pairs (negative set).
    #' The following data consists of:
    #' \itemize{
    #'   \item PPI: SARS-CoV-2-human protein-protein interactions (PPIs)
    #'   \item Official Symbol Interactor A: SARS-CoV-2 gene names
    #'   \item official Symbol Interactor B: human host gene names
    #'   \item Pathogen_Protein: UniProt identifiers for SARS-CoV-2 virus
    #'   \item Host_Protein: UniProt identifiers for human proteins
    #'   \item class: labeled examples (both positive and negative)
    #' }
    #' @details
    #' To construct this dataset, validated interactions (positive set) were
    #' retrieved from BioGrid database and were further filtered to only include
    #' those interactions provided by (Samavarchi-Tehrani et al., 2020).
    #' In this study, the authors mapped interaction between 27 SARS-CoV-2 and
    #' human proteins via the proximity-dependent biotinylation (BioID)
    #' approach. 500 SARS-CoV-2-host interaction pairs then randomly
    #' selected from all pairs to serve as positive examples.
    #' To construct negative examples,negative sampling were used using
    #' \code{\link[HPiP]{get_negativePPI}}.
    #' @name Gold_ReferenceSet
    #' @usage data(Gold_ReferenceSet)
    #' @docType data
    #' @format a data.frame containing 500 validated pairs
    #' (i.e., positive set) and 500 non-interacting pairs (i.e., negative set).
    #' @source
    #' \url{https://www.biorxiv.org/content/10.1101/2020.09.03.282103v1}
    #' @references
    #' Samavarchi-Tehrani,P. et al.
    #' (2020) A SARS-CoV-2-host proximity interactome. BioRxiv.
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