percentMarkerOverlap: percentMarkerOverlap

In fungenomics/cytobox: A toolbox for analyzing single cell RNA-seq data

Description

percentMarkerOverlap

Usage

percentMarkerOverlap(markers1, markers2, mode = "min",
  marker_col = "gene")

Arguments

markers1	Data frame of markers for one dataset as returned by Seurat::FindAllMarkers()
markers2	Data frame of markers for second dataset as returned by Seurat::FindAllMarkers()
mode	"s1", "s2", "min", "max"
marker_col	String specifying the column in the markers data frames which specifies the cluster. By default, Seurat calls this "gene" (the default here); in objects produced by the lab's pipeline, it may be called "external_gene_name".

Value

Data frame with three columns: "s1_cluster" giving the cluster for dataset 1, "s2_cluster" giving the cluster for dataset 2, and "marker_overlap" which gives the computed min percent overlap of markers between the two clusters

Author(s)

Selin Jessa

Examples

percentMarkerOverlap(markers_pbmc, markers_pbmc)

fungenomics/cytobox documentation built on Feb. 13, 2020, 10:51 a.m.