topgenes_extract function

Extract Top Markers

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

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.

Returns

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

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.

Examples

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