idProteinType: A function to determine viable baits, viable preys, or...

In Bioconductor/ppiStats: Protein-Protein Interaction Statistical Package

Description

These functions take a bait to prey directed graphNEL and returns either a character vector of all proteins which participates in homodimer relationships or a list of three character vectors: a vector of viable baits, a vector of viable prey, and a vector of the viable bait/prey.

Usage

idViableProteins(bpGraph, homomer=TRUE)
idHomodimers(bpGraph)

Arguments

bpGraph	A directed graphNEL
homomer	A logical. If True, homomer relationships will also be used to characterize proteins as viable baits, viable prey, and also as viable bait/prey simultaneously. If False, those proteins whose only intraction is a homomer relationship will not be characterized as viable in any context.

Value

The return value for idHomodimers is a character vector of those proteins which participates in homomer relationships.

The return value for idViableProteins is a list of two character vectors:

VB	A vector of baits that finds at least one prey in the experimental graphNEL, i.e. the nodes with out-degree at greater than 0. If homomer = FALSE, those proteins which participate in only homomer relationships will not be returned.
VP	A vector of prey which is found by at least one bait in the experimental graphNEL, i.e. the nodes with in-degree at greater than 0. If homomer = FALSE, those proteins which participate in only homomer relationships will not be returned.
VBP	A vector of proteins that are both viable baits and viable prey in an experimental dataset as defined above. If homomer = FALSE, those proteins which participate in only homomer relationships will not be returned.

Author(s)

T Chiang

Examples

data("ItoCore2001BPGraph", package = "ppiData")
idViableProteins(ItoCore2001BPGraph)
idHomodimers(ItoCore2001BPGraph)

Bioconductor/ppiStats documentation built on Nov. 1, 2021, 1:24 a.m.