compute_nst_scores: Compute non-self talk scores from SingleCellExperiment object

In saezlab/liana: LIANA: a LIgand-receptor ANalysis frAmework

Compute non-self talk scores from SingleCellExperiment object

Description

This function computes the non-self talk scores for all the cell types contained in a SingleCellExperiment object. It iterates through the ligand-receptor pairs that are provided as input and calculates these entropy-based measurements for each cell type using its normalized expression matrix, which should contain log-transformed values.

Usage

compute_nst_scores(
  sce,
  ligand_receptor_df,
  assay.type = "logcounts",
  seed = 1004
)

Arguments

sce	A SingleCellExperiment object containing log-normalized expression values and cell type annotations as colLabels
ligand_receptor_df	A data frame with, at least, two columns named 'ligand' and 'receptor' containing the ligand-receptor pairs to evaluate
assay.type	The name of the data slot containing the log-normalized expression values in the SingleCellExperiment object
seed	random seed

Value

A data frame with the computed non-self-talk score for each ligand-receptor pair on each cell-type.

saezlab/liana documentation built on Nov. 8, 2023, 11:53 a.m.