calculate_cluster_specific_expression: Calculate expression metrics across clusters for a set of...

In VCCRI/scTalk: Single-cell talk - an R package for analysis of cell-cell communication networks from single-cell data.

Description

For a provided set of genes, go through each cluster and calculate the average log2-expression of each gene in the cluster, the percentage of cells expressing the gene in the cluster and the log2 FC difference between the cluster and the remaining clusters. Return a data-frame of the results

Usage

calculate_cluster_specific_expression(
  geneList,
  seurat.object,
  exp.threshold = 0,
  threshold = 0.1,
  cluster.set = NULL
)

Arguments

geneList	a list of genes
exp.threshold	expression threshold for considering a gene expressed in a cell
threshold	Threshold of percentage of cells expressing the gene in a cluster for it to be considered expressed
seurat.obect	a Seurat object with cluster identities
option	set of clusters (default: all in the Seurat object)

Value

a data-frame of results

VCCRI/scTalk documentation built on June 5, 2021, 6:35 a.m.