| cPASS {MSiP} | R Documentation |
cPASS
Description
This function applies Comparative Proteomic Analysis Software Suite (CompPASS) model to score instances (e.g., bait-prey interactions (BPIs) in the data.frame. The CompPASS is a robust statistical scoring scheme for assigning confidence scores to bait-prey interactions (Sowa et al., 2009).This function was based on the source code. https://github.com/dnusinow/cRomppass
Usage
cPASS(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 average peptide spectrum match (PSMs), total PSMs, ratio total PSMs,Z-score,S-score,D-score and WD-score.
Author(s)
Matineh Rahmatbakhsh, matinerb.94@gmail.com
References
Huttlin, E. L., Ting, L., Bruckner, R. J., Gebreab, F., Gygi, M. P., Szpyt, J., et al. (2015). The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 162, 425-440.
Sowa, M. E., Bennett, E. J., Gygi, S. P., and Harper, J. W. (2009). Defining the human deubiquitinating enzyme interaction landscape. Cell 138, 389-403.
Examples
data(SampleDatInput)
datScoring <- cPASS(SampleDatInput)
head(datScoring)