calculate.gene.counts: Get expressed genes from pseudobulk

In heiniglab/scPower: Experimental design framework for scRNAseq population studies (eQTL and DE)

Get expressed genes from pseudobulk

Description

Return a data frame with all genes, which are defined as expressed per cell type (at least min.counts in perc.indiv.expr fraction of all individuals)

Usage

calculate.gene.counts(expr.array, min.counts = 3, perc.indiv.expr = 0.5)

Arguments

expr.array	3d pesudobulk matrix of genes x individuals x cell type (output of create.pseudobulk)
min.counts	More than is number of UMI counts for each gene per individual and cell type is required to defined it as expressed in one individual
perc.indiv.expr	Percentage of individuals that need to have this gene expressed to define it as globally expressed

Value

Data frame with all expressed genes per cell type (columns: gene name, cell type, fraction in how many samples the gene is expressed)

heiniglab/scPower documentation built on Jan. 9, 2025, 12:13 p.m.