FindFilteredMarkers: Find marker genes for a given set of cells, and filter out...

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

Find marker genes for a given set of cells, and filter out highly expressed genes from cells in a reference Seurat object.

Description

Used to filter candidate marker genes for a subcluster Seurat object. Prevents markers from being chosen if they are highly expressed in other celltypes.

Usage

FindFilteredMarkers(
  obj.1 = NULL,
  obj.2 = NULL,
  ident.1 = "seurat_clusters",
  ident.2 = "seurat_clusters",
  de.method = "wilcox",
  fdr.cutoff = 0.05,
  log2fc.cutoff = 0.25,
  perc.cutoff = 0.9,
  extra.cell.filter = NULL
)

Arguments

obj.1	The object containing clusters that you want marker genes for. Defaults to NULL.
obj.2	The object containing reference data against which we'll filter the markers in obj.1. Defaults to NULL.
ident.1	The group identifier for obj.1. Defaults to "seurat_clusters".
ident.2	The group identifier for obj.2. Defaults to "seurat_clusters".
de.method	The differential expression method used in FindAllMarkers. Defaults to "wilcox".
fdr.cutoff	The cutoff used to remove DE genes with non-significant adjusted p-values. Defaults to 0.05.
log2fc.cutoff	The log2FC cutoff used, in part, to determine whether a gene is differentially expressed. Defaults to 0.25.
perc.cutoff	The percentile cutoff used to find highly expressed genes in other cluster. Defaults to 0.9.
extra.cell.filter	An optional list of extra cells to filter out of obj.2 other than the cells in obj.1. Defaults to NULL.

Value

A data.frame of markers for each cluster in obj.1 filtered by genes considered highly expressed in clusters in obj.2.

Author(s)

Jack Leary

See Also

FindSpecificMarkers

FindAllMarkers

Examples

## Not run: 
FindFilteredMarkers(obj.1 = subclust_obj,
                    obj.2 = full_obj,
                    ident.1 = "label",
                    ident.2 = "seurat_clusters")
FindFilteredMarkers(obj.1 = subclust_obj,
                    obj.2 = full_obj,
                    de.method = "t",
                    fdr.cutoff = 0.01,
                    log2fc.cutoff = 1,
                    perc.cutoff = 0.95)

## End(Not run)

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