identify_cluster: identify_cluster

In SShan2021/seuratExtension: Functions based on Seurat

Description

(All)Goes through given top markers and extract those that match the cluster identifiers.

Usage

identify_cluster(
  topmarkers,
  upper = "na",
  top20 = "na",
  writecsv = "na",
  nameoffile = "topmarkers.csv"
)

Arguments

topmarkers	A dataset of topmarkers
upper	upper = "upper" if cells are upper case
top20	top20 = "top20" if only want to consider top 20 markers per cluster
writecsv	writecsv = "writecsv" if want to have csv of top 20 markers per cluster
nameoffile	Put name of what you want to name the output in " ".

Value

A data frame object that has all the markers and corresponding clusters and the cluster type for each gene.

Examples

output_table <- identify_cluster(topmarkers, upper = "upper", top20 = "top20", writecsv = "writecsv",
nameoffile = "topmarkers_40pc_04res.csv")

SShan2021/seuratExtension documentation built on Dec. 18, 2021, noon