GenerateNullPANDADistribution: Generate a null distribution of edge scores for PANDA-like...

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Generate a null distribution of edge scores for PANDA-like networks; that is, the set of edges where (1) the TF does not have a binding motif in the gene region, (2) the TF does not form a complex with any other TF that has a binding motif in the gene region, and (3) the genes regulated by the TF are not coexpressed with the gene in question. We obtain this by inputting an empty prior and an identity coexpression matrix.

Description

Generate a null distribution of edge scores for PANDA-like networks; that is, the set of edges where (1) the TF does not have a binding motif in the gene region, (2) the TF does not form a complex with any other TF that has a binding motif in the gene region, and (3) the genes regulated by the TF are not coexpressed with the gene in question. We obtain this by inputting an empty prior and an identity coexpression matrix.

Usage

GenerateNullPANDADistribution(
  ppiFile,
  motifFile,
  sampSize = 20,
  numberOfPandas = 10
)

Arguments

ppiFile	The location of the protein-protein interaction network between transcription factors. This should be a TSV file where the first two columns are the transcription factors and the third is whether there is a PPI between them.
motifFile	The location of the motif prior from genes to transcription factors. This should be a TSV file where the first column is the transcription factors, the second is the genes, and the third is whether the transcription factor's binding motif is in the gene promoter region.
sampSize	Number of samples to simulate
numberOfPandas	Number of null PANDA networks to generate

netZoo/netZooR documentation built on July 28, 2024, 6 p.m.