findSPERsignals: Find the putative paracrine signals based on SPER scores

In tsinghua-ZTX/SPER: Spatial Paired Expression Ratio

Find the putative paracrine signals based on SPER scores

Description

This function helps find the potential signals based on the given threshold in both SPER scores and expression prevalence. One can provide the marker (cell-type-specific) gene list and ligand-receptor pair data to limit the search range and get a more precise result.

Usage

findSPERsignals(
  target.cell,
  score.mat,
  expr.frac.mat,
  marker.gene = NULL,
  gene.set = NULL,
  LRP.data = NULL,
  score.threshold = 1.5,
  expr.fraction = 0.15
)

Arguments

target.cell	Target ell Type Name
score.mat	Score matrix (SPER, or correlations)
expr.frac.mat	Expression prevalence matrix: matrix values from 0 to 1, showing the percentage of cells in that cell type expressing the gene.
marker.gene	The marker gene matrix with a column 'Type' indicating the cell type information and 'Gene' indicating the gene ID
gene.set	The gene list of interest: could be extracellular or ligand gene sets
LRP.data	Ligand-receptor pair data; used to find the receptors of found paracrine signals; should contain at least two columns: 'gene1' for the ligands and 'gene2' for receptors
score.threshold	Threshold on the score: pairs whose scores larger than the threshold will be kept
expr.fraction	Threshold on expression prevalence: pairs whose prevalence smaller than the threshold will be kept

Value

A gene list containing the spatial dependent genes; if LRP data provided, return a data frame containing both ligand and receptor information

tsinghua-ZTX/SPER documentation built on June 7, 2024, 5:30 a.m.