seurat_to_generes: Identify all cell-type markers

In DustinSokolowski/scMappR: Single Cell Mapper

Description

Takes processed Seurat matrix and identifies cell-type markers with FindMarkers.

Usage

seurat_to_generes(pbmc, test = "wilcox")

Arguments

pbmc	Processed Seurat object.
test	statistical test for calling CT markers – must be in Seurat

Details

Internal: This function runs the FindMarkers function from seurat in a loop, will use the Seurat v2 or Seurat v3 object after identifying which Seurat object is inputted. It then takes the output of the FindMarkers and puts it in a list, returning it.

Value

seurat_to_generes A list of genes where their over-representation in the i'th cell-type is computed. Each element contains the gene name, adjusted p-value, and the log2Fold-Change of each gene being present in that cell-type.

Examples

  
 
data(sm)
toProcess <- list(example = sm)
tst1 <- process_from_count(toProcess, "testProcess")
generes <- seurat_to_generes(tst1)

DustinSokolowski/scMappR documentation built on July 7, 2020, 5:44 p.m.