get_negativePPI: Construct Negative Reference Host-Pathogen Protein-Protein...

In mrbakhsh/HPiP: Host-Pathogen Interaction Prediction

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, [e-mail]

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)

mrbakhsh/HPiP documentation built on March 28, 2023, 4:35 p.m.