cPASS: cPASS

In Babulab-bioc/MSiP: 'MassSpectrometry' Interaction Prediction

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, [e-mail]

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)

Babulab-bioc/MSiP documentation built on Dec. 17, 2021, 9:52 a.m.