scMappR (version 1.0.11)

seurat_to_generes: Identify all cell-type markers

Description

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

Usage

seurat_to_generes(pbmc, test = "wilcox")

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.

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.

Examples

# \donttest{  
 
data(sm)
toProcess <- list(example = sm)
tst1 <- process_from_count(countmat_list = toProcess,name = "testProcess",
                          theSpecies = "mouse")
generes <- seurat_to_generes(pbmc = tst1)
# }