seurat_to_generes {scMappR} | R Documentation |
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")
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(countmat_list = toProcess,name = "testProcess",
theSpecies = "mouse")
generes <- seurat_to_generes(pbmc = tst1)
[Package scMappR version 1.0.11 Index]