filter_incohrent_TF_target: filter_incohrent_TF_target

In saezlab/COSMOS: COSMOS (Causal Oriented Search of Multi-Omic Space)

filter_incohrent_TF_target

Description

Filters incoherent target genes from a regulatory network based on a decoupling analysis of upstream and downstream gene expression.

Usage

filter_incohrent_TF_target(
  decouplRnival_res,
  TF_reg_net,
  meta_network,
  RNA_input
)

Arguments

decouplRnival_res	A data frame resulting from the decoupleRnival function.
TF_reg_net	A data frame containing prior knowledge of transcription factor (TF) regulatory interactions.
meta_network	A network data frame containing signed directed prior knowledge of molecular interactions.
RNA_input	A named vector containing differential gene expression data.

Value

A network data frame containing the genes that are not incoherently regulated by TFs.

Examples

# Example input data
upstream_input <- c("A" = 1, "B" = -1, "C" = 0.5)
downstream_input <- c("D" = 2, "E" = -1.5)
meta_network <- data.frame(
  source = c("A", "A", "B", "C", "C", "D", "E"),
  target = c("B", "D", "D", "E", "D", "B", "A"),
  interaction = c(-1, 1, -1, 1, -1, -1, 1)
)
RNA_input <- c("A" = 1, "B" = -1, "C" = 5, "D" = -0.7, "E" = -0.3)

TF_reg_net <- data.frame(
source = c("B"),
target = c("D"),
mor = c(-1)
)

# Run the decoupleRnival function to get the upstream influence scores
upstream_scores <- decoupleRnival(upstream_input, downstream_input, meta_network, n_layers = 2, n_perm = 100)

filtered_network <- filter_incohrent_TF_target(upstream_scores, TF_reg_net, meta_network, RNA_input)

print(filtered_network)

saezlab/COSMOS documentation built on Sept. 17, 2023, 1:22 p.m.