projectAndRecombine: Perform network projecting on network when the network genes...

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

Perform network projecting on network when the network genes and the experiment genes aren't exactly the same.

Description

The gene network might be defined only on a subset of genes that are measured in any experiment. Further, an experiment might not measure all genes that are present in the network. This function projects the experiment data onto the gene space defined by the network prior to projecting. Then, it projects the projected data back into the original dimansions.

Usage

projectAndRecombine(
  gene_expression,
  adj_matrix,
  alpha,
  projecting.function = randomWalkBySolve,
  normalizeAdjMatrix = c("rows", "columns")
)

Arguments

gene_expression	gene expession data to be projected [N_genes x M_samples]
adj_matrix	adjacenty matrix of network to perform projecting over. Will be column-normalized. Rownames and colnames should be genes.
alpha	network projecting parameter (1 - restart probability in random walk model.
projecting.function	must be a function that takes in data, adjacency matrix, and alpha. Will be used to perform the actual projecting.
normalizeAdjMatrix	which dimension (rows or columns) should the adjacency matrix be normalized by. rows corresponds to in-degree, columns to out-degree.

Value

matrix with network-projected gene expression data. Genes that are not present in projecting network will retain original values.

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