get_negativePPI {HPiP} | R Documentation |
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).
get_negativePPI(prot1, prot2, TPset)
prot1 |
A character vector containing pathogen proteins. |
prot2 |
A character vector containing host proteins. |
TPset |
A character vector containing positive reference interactions. |
get_negativePPI
A Data.frame containing true negative interactions.
Matineh Rahmatbakhsh, matinerb.94@gmail.com
Eid, F.-E., ElHefnawi, M., and Heath, L. S. (2016). DeNovo: virus-host sequence-based protein–protein interaction prediction. Bioinformatics 32, 1144–1150.
See get_positivePPI
for generating positive
protein-protein interaction.
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)