get_negativePPI {HPiP} | R Documentation

## Construct Negative Reference Host-Pathogen Protein-Protein Interactions (HP-PPIs)

### Description

Construct true negative protein-protein interactions from the positive interactions. In the context of PPI prediction, a negative interaction is a pair of proteins that unlikely to interact. Since there is no experimentally verified non-interacting pair, the negative sampling can be used to construct the negative reference set. The negative sampling can be constructed from a set of host proteins, a set of pathogen proteins, and a list of positive reference interactions between members of host and pathogen proteins (Eid et al., 2016).

### Usage

    get_negativePPI(prot1, prot2, TPset)

### Arguments

`prot1` | A character vector containing pathogen proteins.
`prot2` | A character vector containing host proteins.
`TPset` | A character vector containing positive reference interactions.

### Details

get_negativePPI

### Value

A Data.frame containing true negative interactions.

### Author(s)

Matineh Rahmatbakhsh, matinerb.94@gmail.com

### References

Eid, F.-E., ElHefnawi, M., and Heath, L. S. (2016). DeNovo: virus-host sequence-based protein–protein interaction prediction. Bioinformatics 32, 1144–1150.

### See Also

See `get_positivePPI` for generating positive protein-protein interaction.

### Examples

    prot1 <- c("P0DTC4", "P0DTC5", "P0DTC9")
    prot2 <- c("Q9Y679", "Q9NW15", "Q9NXF8")
    TPset <- c("P0DTC4~P31948", "P0DTC8~Q13438")
    TN_PPI <- get_negativePPI(prot1, prot2, TPset)
    head(TN_PPI)

[Package HPiP version 1.0.0 Index]