Get the regulatory network.

Get the regulatory network.

getNetwork(
  sample,
  tf,
  peak2gene,
  p2g_cutoff = 0.5,
  motif2gene,
  targets = 1,
  level = 2
)

Arguments

sample

The sample name. Only one sample support.

tf

The motif ID. Only one motif support.

peak2gene

The RDS file obtained by **getPeak2Gene**.

p2g_cutoff

The absolute cutoff of peak2gene correlation. Default: 0.5.

motif2gene

The annotation file obtained by **getMotif2Gene**.

targets

The target only contain TF(1) or contain genes and TFs (2). Default: 1.

level

Consider only the target genes of your TF of interest (1). Consider not only the target genes of your TF of interest, but also more downstream target genes (2). Default: 2.

Examples

 getNetwork(sample="Bulk_B", tf="Atf1_MA0604.1", peak2gene="All_Peak2Gene_links.rds", p2g_cutoff = 0.5, motif2gene = m2g)
#> Warning: cannot open compressed file 'All_Peak2Gene_links.rds', probable reason 'No such file or directory'
#> Error in gzfile(file, "rb"): cannot open the connection