topgenes_extract {scMappR}

Extract Top Markers

Description

Internal – Extracts strongest cell-type markers from a Seurat object.

Usage

topgenes_extract(generes, padj = 0.05, FC = 1.5, topNum = 30)

Arguments

generes

A list of cell-type markers with fold-changes and p-values (FindMarkers output in Seurat).

padj

The p-value (FDR) cutoff.

FC

The fold-change cutoff.

topNum

The number of genes to extract.

Details

Internal, this function runs through a list of outputs from FindMarkers objects in Seurat and will extract genes past a padj and fold-change threshold. Then it extracts the topNum number of genes. if you have not used the FindMarkers function, then a list of summary statistics with fold-change designated by avg_logFC and p-val by p_val_adj.

Value

topgenes_extract Returns a list of character vectors with the top (topNum) of gene markers for each cell-type.

Examples

 
 
 # load generes object
 data(POA_example)
 topGenes <- topgenes_extract(generes = POA_example$POA_generes)