intersect_regulons: Intersect network target features with input matrix.

In saezlab/decoupleR: decoupleR: Ensemble of computational methods to infer biological activities from omics data

Intersect network target features with input matrix.

Description

Keep only edges which its target features belong to the input matrix.

Usage

intersect_regulons(mat, network, .source, .target, minsize)

Arguments

mat	Matrix to evaluate (e.g. expression matrix). Target nodes in rows and conditions in columns. rownames(mat) must have at least one intersection with the elements in network .target column.
network	Tibble or dataframe with edges and it's associated metadata.
.source	Column with source nodes.
.target	Column with target nodes.
minsize	Minimum number of targets per source allowed.

Value

Filtered tibble.

Examples

inputs_dir <- system.file("testdata", "inputs", package = "decoupleR")
mat <- readRDS(file.path(inputs_dir, "mat.rds"))
net <- readRDS(file.path(inputs_dir, "net.rds"))
intersect_regulons(mat, net, source, target, minsize=4)

saezlab/decoupleR documentation built on Oct. 21, 2024, 8:47 a.m.