GetTopMarkersDF: Get Top Differential Expression Genes Data Frame

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

Get Top Differential Expression Genes Data Frame

Description

Retrieves a data frame of the top N differentially expressed genes from differential gene expression analysis results, offering an option to exclude certain genes based on patterns.

Usage

GetTopMarkersDF(
  dfDE = df.markers,
  n = p$n.markers,
  order.by = c("avg_log2FC", "p_val_adj")[1],
  exclude = c("^A[CFLP][0-9]{6}", "^Z[0-9]{5}", "^LINC0[0-9]{4}", "^C[1-9]+orf[1-9]+",
    "[-|\\.]AS[1-9]*$", "[-|\\.]DT[1-9]*$", "^MIR[1-9]", "^SNHG[1-9]")
)

Arguments

dfDE	Data frame containing the results of differential gene expression analysis (e.g., output from FindAllMarkers()). Default: df.markers.
n	Number of top markers to retrieve per cluster. Default: p$n.markers.
order.by	Priority column for sorting markers before selection, such as "avg_log2FC"; Default: "avg_log2FC".
exclude	Vector of regex patterns to exclude genes from the top markers list; Default: c("^AL*|^AC*|^LINC*").

See Also

FindAllMarkers, arrange, filter, group_by

Examples

## Not run: 
if (interactive()) {
  topMarkersDF <- GetTopMarkersDF(dfDE = df.markers, n = 3)
}

## End(Not run)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.