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Identify top expressed genes in the dataset

Source: R/SpotDetect.R
GetTopGenes.Rd

This function identifies the top expressed genes either globally or grouped by sample and/or cell type. Useful for finding marker genes or highly expressed pathogen genes.

Usage

GetTopGenes(
  STID_obj,
  top_n = 10,
  pattern = NULL,
  grp_by_samp = FALSE,
  grp_by_celltype = FALSE,
  assay_id = "Spatial",
  layer_id = "counts"
)

Arguments

STID_obj

A Seurat or STID object

top_n

Numeric, number of top genes to return (default: 10)

pattern

Character, regular expression pattern to filter genes (default: NULL)

grp_by_samp

Logical, whether to group by sample (default: FALSE)

grp_by_celltype

Logical, whether to group by cell type (default: FALSE)

assay_id

Character, name of the assay to use (default: "Spatial")

layer_id

Character, name of the layer/data slot to use (default: "counts")

Value

If no grouping, returns a character vector of top genes. If grouping, returns a named list of top genes per group.

Examples

if (FALSE) { # \dontrun{
# Get top 20 genes globally
top_genes <- GetTopGenes(STID_obj = STID_object, top_n = 20)

# Get top 10 pathogen genes per sample
pathogen_genes <- GetTopGenes(
  STID_obj = STID_object,
  top_n = 10,
  pattern = "^VP",
  grp_by_samp = TRUE
)
} # }