scCustomize (version 3.1.3)

Extract_Top_Markers: Extract Top N Marker Genes

Description

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

Usage

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
)

Value

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

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.

Examples

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