cellnetworksPPI: Create a weighted protein-protein interaction network based...

In edroaldo/fusca: Framework for Unified Single-Cell Analysis

Create a weighted protein-protein interaction network based on cell-type specific correlation coefficients.

Description

Create a graph based on gene expression correlation for the protein-protein interactions for each population. The edges are the intersection of the ones in the protein-protein interaction network and the ones obtained from the correlation of gene expression in the cells, the weights are the correlation value. The edge lists are saved to files.

Usage

cellnetworksPPI(
  ppi,
  expr,
  samples,
  corThr = 0,
  column,
  dir.prefix = "results/paths"
)

Arguments

ppi	igraph graph; the network as calculated by the createPPI function.
expr	dgCMatrix; gene expression in each cell, found in CellRouter@ndata.
samples	data frame; the metadata information of the cells, found in CellRouter@sampTab.
corThr	numeric; correlation threshold.
column	character; character; column in the metadata table to specify how the data should be aggregated (e.g. per cell type, cluster or other metadata available).
dir.prefix	character; prefix of the directory where the files will be saved.

Value

list; the networks (igraph objects) for each cell type/cluster/other metadata.

edroaldo/fusca documentation built on March 1, 2023, 1:43 p.m.