cellnetworksPPI2: 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. A more efficient version of cellnetworksPPI.

Usage

cellnetworksPPI2(
  ppi,
  expr,
  samples,
  corThr1,
  corThr2,
  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.
corThr1	numeric; values smaller then corThr1 in the correlation matrix will be replaced by 0. Therefore, there will be no connections between the genes with value 0.
corThr2	numeric; keep gene-gene interactions with correlation higher than the 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.