projectData: Project gene expression data onto a protein-protein...

In sqjin/CellChat: Inference and analysis of cell-cell communication from single-cell and spatial transcriptomics data

Project gene expression data onto a protein-protein interaction network

Description

A diffusion process is used to smooth genes’ expression values based on their neighbors’ defined in a high-confidence experimentally validated protein-protein network.

Usage

projectData(
  object,
  adjMatrix,
  alpha = 0.5,
  normalizeAdjMatrix = c("rows", "columns")
)

Arguments

object	CellChat object
adjMatrix	adjacency matrix of protein-protein interaction network to use
alpha	numeric in [0,1] alpha = 0: no smoothing; a larger value alpha results in increasing levels of smoothing.
normalizeAdjMatrix	how to normalize the adjacency matrix possible values are 'rows' (in-degree) and 'columns' (out-degree)

Details

This function is useful when analyzing single-cell data with shallow sequencing depth because the projection reduces the dropout effects of signaling genes, in particular for possible zero expression of subunits of ligands/receptors

Value

a projected gene expression matrix

sqjin/CellChat documentation built on Nov. 10, 2023, 4:29 a.m.