cellMarker: assign cell type based on cell cluster results
In guokai8/rcellmarker: Identify cell type based on cell markers

cellMarker

R Documentation

assign cell type based on cell cluster results

Description

assign cell type based on cell cluster results

Usage

cellMarker(
  x,
  type = "seurat",
  species = "human",
  keytype = "SYMBOL",
  weight = NULL,
  format = "long",
  cluster = NULL,
  tissue = NULL,
  topn = 3,
  padj = 0.05,
  minSize = 3,
  maxSize = 500,
  padj.method = "BH"
)

Arguments

`x`	input file for marker annotation
`type`	source of marker genes (seurat(default), cellranger, custom)
`species`	species for annotation
`keytype`	keytype for input genes
`weight`	weight threshold for marker filtering
`format`	file format for user supplied data.frame(long: Cluster, gene; wide: gene, following cluster name as column name)
`cluster`	clutser number (default: NULL for annotate all clusters)
`tissue`	tissue for annotation (default: NULL to use all tissues)
`topn`	the number of cell type to list fro each cluster
`padj`	adjust p value threshold
`minSize`	minimal number of genes included in significant cell type
`maxSize`	maximum number of genes included in significant cell type
`padj.method`	pvalue adjust method(default: "BH")