Weighted.matrixModel {MSiP} | R Documentation |
Weighted.matrixModel
Description
This function computes the weighted matrix model for instances (e.g., bait-prey interactions (BPIs)) in the data.frame.The output of the weighted matrix model includes the number of experiments for which the pair of proteins is co-purified (i.e., k) and -1*log(P-value) of the hypergeometric test (i.e., logHG) given the experimental overlap value, each protein's total number of observed experiments, and the total number of experiments (Drew et al., 2017).
Usage
Weighted.matrixModel(datInput)
Arguments
datInput |
Data frame with column names: Experiment.id, Replicate, Bait, Prey, and count (i.e., prey count). |
Value
Data frame containing bait-prey pairs with k (i.e.,number of co-purifications) & logHG (i.e., $-1$*log(P-val) of the hypergeometric test)
Author(s)
Matineh Rahmatbakhsh, matinerb.94@gmail.com
References
Drew, K., Lee, C., Huizar, R. L., Tu, F., Borgeson, B., McWhite, C. D., et al. (2017). Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. Mol. Syst. Biol. 13, 932.
Examples
data(SampleDatInput)
datScoring <- Weighted.matrixModel(SampleDatInput)
head(datScoring)