FindSpecificMarkers: Find highly specific marker genes for all clusters in a...

In jr-leary7/SCISSORS: Identify cell subpopulations in single cell RNA-seq data

Find highly specific marker genes for all clusters in a Seurat object.

Description

This function finds marker genes for all clusters, and then filters those markers on a per-cluster basis against the most highly expressed genes in other clusters.

Usage

FindSpecificMarkers(
  seurat.object = NULL,
  assay.use = "RNA",
  slot.use = "data",
  ident.use = "seurat_clusters",
  de.method = "wilcox",
  perc.cutoff = 0.9,
  log2fc.cutoff = 0.25,
  fdr.cutoff = 0.05
)

Arguments

seurat.object	The Seurat object containing clusters for which you'd like marker genes identified. Defaults to NULL.
assay.use	The assay to use when testing. Defaults to "RNA".
slot.use	The matrix to use when testing. Defaults to "data", for normalized counts, but "counts" (for the raw counts) can also be used.
ident.use	The cell identity to group by. Defaults to "seurat_clusters".
de.method	The differential expression method used in FindAllMarkers. Defaults to "wilcox".
perc.cutoff	The percentile cutoff used to find highly expressed genes in other cluster. Defaults to 0.9.
log2fc.cutoff	The log2FC cutoff used, in part, to determine whether a gene is differentially expressed. Defaults to 0.25.
fdr.cutoff	The cutoff used to remove DE genes with non-significant adjusted p-values. Defaults to 0.05.

Value

A data.frame of markers for each cluster filtered by genes considered highly expressed in other clusters.

Author(s)

Jack Leary

See Also

FindAllMarkers

Examples

## Not run: 
FindSpecificMarkers(seurat_object,
                    method = "wilcox",
                    ident.use = "celltype")
FindSpecificMarkers(seurat_object,
                    method = "wilcox",
                    assay.use = "SCT",
                    slot.use = "data")

## End(Not run)

jr-leary7/SCISSORS documentation built on April 20, 2023, 8:21 p.m.