recordSticky {simulatorAPMS}R Documentation

This function records proteins known to be sticky in the simulation of AP-MS.

Description

In the actual AP-MS technology, sticky proteins are identified and then removed from the process so sticky proteins do not influence the outcome of the protein-protein co-membership matrix nor the estimate from complex composition algorithms such as apComplex.

Usage

recordSticky(simMat, vSticky, vBaits)

Arguments

simMat An adjcency matrix: the rows are indexed by bait proteins and the colunms are indexed by prey proteins
vSticky The pre-determined vector of sticky proteins
vBaits A character vector of the proteins used as baits

Details

The recordSticky function will return both the sticky proteins that are put into the function at the beginning as well as proteins which pull down a large number of prey proteins.

Value

A character vector:
The return value is a vector of all the proteins that are considered to be sticky in the simulation of AP-MS

Author(s)

Tony Chiang

Examples

library(simulatorAPMS)
data(fullSimEX)
data(vBaitsEX)
recordSticky(fullSimEX, c(vBaitsEX[2], vBaitsEX[3]))

[Package simulatorAPMS version 1.8.0 Index]