corto (version 1.3.1)

getregulon: getregulon - Flatten a Regulon Object into a Table

Description

Converts a regulon into a data frame of edges, one row per centroid-target pair, optionally written to a tab-separated file.

Usage

getregulon(
  regulon,
  tf_list = NULL,
  likelihood_threshold = 0,
  export = FALSE,
  filename = "regulon.tsv"
)

Value

A data frame with columns tf, target, correlation and likelihood

Arguments

regulon

A regulon object, as generated by corto()

tf_list

A character vector of centroid names to keep. Default is NULL, i.e. all centroids

likelihood_threshold

Minimum edge likelihood, between 0 and 1. Default is 0

export

A logical value. If TRUE the table is also written to file. Default is FALSE

filename

The file to write when export is TRUE. Default is "regulon.tsv"

Examples

load(system.file("extdata","inmat.rda",package="corto",mustWork=TRUE))
load(system.file("extdata","centroids.rda",package="corto",mustWork=TRUE))
regulon<-corto(inmat,centroids=centroids,nbootstraps=10,p=1e-30,nthreads=2)
edges<-getregulon(regulon)
head(edges)