Extract Top N Marker Genes — Extract_Top

Extract vector gene list (or named gene vector) from data.frame results of FindAllMarkers or similar analysis.

Extract_Top_Markers(
  marker_dataframe,
  num_features = 10,
  num_genes = deprecated(),
  group_by = deprecated(),
  group.by = "cluster",
  rank_by = "avg_log2FC",
  gene_column = "gene",
  gene_rownames_to_column = FALSE,
  data_frame = FALSE,
  named_vector = TRUE,
  make_unique = FALSE
)

Arguments

marker_dataframe: data.frame output from FindAllMarkers or similar analysis.
num_features: number of features per group (e.g., cluster) to include in output list.
num_genes: soft-deprecated. See num_features.
group_by: soft-deprecated. See group.by.
group.by: column name of marker_dataframe to group data by. Default is "cluster" based on FindAllMarkers.
rank_by: column name of marker_dataframe to rank data by when selecting num_genes per group.by. Default is "avg_log2FC" based on FindAllMarkers.
gene_column: column name of marker_dataframe that contains the gene IDs. Default is "gene" based on FindAllMarkers.
gene_rownames_to_column: logical. Whether gene IDs are stored in rownames and should be moved to column. Default is FALSE.
data_frame: Logical, whether or not to return filtered data.frame of the original markers_dataframe or to return a vector of gene IDs. Default is FALSE.
named_vector: Logical, whether or not to name the vector of gene names that is returned by the function. If TRUE will name the vector using the column provided to group.by. Default is TRUE.
make_unique: Logical, whether an unnamed vector should return only unique values. Default is FALSE. Not applicable when data_frame = TRUE or named_vector = TRUE.

Value

filtered data.frame, vector, or named vector containing gene IDs.

Examples

if (FALSE) {
top10_genes <- Extract_Top_Markers(marker_dataframe = markers_results, num_genes = 10,
group.by = "cluster", rank_by = "avg_log2FC")
}