getExpressedGenes: Identify expressed genes

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Identify expressed genes

Description

Identify expressed genes in Seurat object.

Usage

getExpressedGenes(
  object,
  min.pct = 0.1,
  min.cell = NULL,
  group = NA,
  group.boolean = "OR"
)

Arguments

object	Seurat Object
min.pct	minimum expressing fraction. Default: 0.1. Ignored if min.cell is specified.
min.cell	minimum number of expressing cells. If specified, min.pct is ignored.
group	Character specifying metadata field to group cells by. If not specified, global expression fraction is evaluated. If specified, group-level gene lists are combined used group.boolean.
group.boolean	Boolean used to combine group genelists. One of "OR" or "AND". Default: "OR". Argument is ignored if 'group' is not specified.

Value

vector of gene names

Author(s)

Nicholas Mikolajewicz

Examples

split.var <- "seurat_clusters"
which.genes <- getExpressedGenes(object = so.query, min.pct = 0.1, group = split.var, group.boolean = "OR")

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.