CompPASS: CompPASS

In zqzneptune/SMAD: Statistical Modelling of AP-MS Data (SMAD)

CompPASS

Description

CompPASS Comparative Proteomic Analysis Software Suite (CompPASS) is based on spoke model. This algorithm was developed by Dr. Mathew Sowa for defining the human deubiquitinating enzyme interaction landscape (Sowa, Mathew E., et al., 2009). The implementation of this algorithm was inspired by Dr. Sowa's online tutorial (http://besra.hms.harvard.edu/ipmsmsdbs/cgi-bin/tutorial.cgi). The output includes Z-score, S-score, D-score and WD-score. This function also computes entropy and normalized WD-score. The source code for this function was based on the source code. https://github.com/dnusinow/cRomppass

Usage

CompPASS(datInput)

Arguments

datInput

A dataframe with column names: idRun, idBait, idPrey, countPrey. Each row represent one unique protein captured in one pull-down experiment

Value

A data frame consists of unique bait-prey pairs with Z-score, S-score,D-score and WD-score indicating interacting probabilities.

Author(s)

Qingzhou Zhang, [e-mail]

References

Sowa, Mathew E., et al. "Defining the human deubiquitinating enzyme interaction landscape." Cell 138.2 (2009): 389-403. https://doi.org/10.1016/j.cell.2009.04.042

Huttlin, Edward L., et al. "The BioPlex network: a systematic exploration of the human interactome." Cell 162.2 (2015): 425-440. https://doi.org/10.1016/j.cell.2015.06.043

Huttlin, Edward L., et al. "Architecture of the human interactome defines protein communities and disease networks." Nature 545.7655 (2017): 505. https://www.nature.com/articles/nature22366

Examples

data(TestDatInput)
datScore <- CompPASS(TestDatInput)
head(datScore)

zqzneptune/SMAD documentation built on Nov. 6, 2024, 1:53 p.m.