find_markers: Function to extract cluster specific genes from reference...

In BatadaLab/scID: geneset-guided identification of cell types using single cell RNA-seq data

Description

Function to extract cluster specific genes from reference clusters. This function uses MAST test as implemented in the Seurat package.

Usage

find_markers(
  reference_gem,
  reference_clusters,
  logFC,
  only.pos,
  normalize_reference
)

Arguments

reference_gem	Data frame of gene expression (rows) per cell (columns) in reference data
reference_clusters	Named list of cluster IDs of reference cells
logFC	Log2FC threshold for extracting markers from reference clusters
only.pos	Logical to include negative markers in the cluster specific gene sets
normalize_reference	Logical to select if reference data need to be normalized (when raw counts have been provided)

Value

Data frame of cluster specific genes extracted

BatadaLab/scID documentation built on Oct. 21, 2021, 3:06 p.m.