getGeneticInteractome: getGeneticInteractome

In hyginn/BCB420.2019.ESA: Exploratory Systems Analysis Tools

Description

getGeneticInteractome

Usage

getGeneticInteractome(mySys, criterion)

Arguments

mySys	(dataframe) A 2-column dataframe of PPI between system's components.
criterion	(string) Either "stringent" or "relaxed", specifying whether only GGI between physical interactors should be selected.

Value

(dataframe) A 3-column dataframe of PPIs and either the GGIs between them (iff criterion == "stringent") or all GGIs that implicate them (iff relaxed == "stringent"). The first two columns denote the interacting pair; the third is the type of genetic interaction.

Author(s)

Nada Elnour, [e-mail]

getGeneticInteractome augments systems with BioGRID genetic interaction annotations

Examples

## Not run: 
library(data.table)
biogrid <- fetchData("BioGRID")
url <- paste0("http://www.informatics.jax.org/go/report.txt?",
              "goID=GO:0006099&results=42&startIndex=0&sort=term&dir=")
myGenes <- fread(url)
myGenes <- myGenes$`MGI Gene/Marker ID`
myGenes <- toupper(myGenes)
PPI <- biogrid[biogrid$type == "physical", ]
sel <- PPI$A %in% myGenes & PPI$B %in% myGenes
mySys <- PPI[sel, ]
ppi_ggi <- getGeneticInteractome(mySys, "stringent")
network <- getGeneticInteractome(mySys, "relaxed")
hypothesize(network, ppi_ggi)

## End(Not run)

hyginn/BCB420.2019.ESA documentation built on May 29, 2019, 1:23 p.m.