myfindmarkers: To get the top DE gene of cluster

In Lian-Lab/LIANLAB: To integrate analysis methods and simplify analysis process

Description

To get the top DE gene of cluster

Usage

myfindmarkers(
  seurat_object,
  filename = NULL,
  thresh.use = 0.25,
  species = "human",
  all.markers = NULL,
  colors = NULL
)

Arguments

seurat_object	seurat.obj
filename	the name of the generated file
thresh.use	Limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells
species	the species of the seurat.obj
all.markers	the result of the FindAllMarkers()
colors	the colors of clusters

Value

a list including two characters,top5 and top20

Examples

## Not run: 
input.file <- system.file('extdata','pbmc_1k.RDS',package = 'LIANLABDATA')
pbmc_1k <- readRDS(input.file)
top_genes <- myfindmarkers(pbmc_1k)

## End(Not run)

Lian-Lab/LIANLAB documentation built on June 23, 2021, 5:37 a.m.