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Find Marker Genes for Differentially Abundant Neighborhoods

find_markers.Rd

Identifies marker genes for differentially abundant neighborhoods.

Usage

find_markers(
  all_results,
  samples,
  celltype_var,
  celltypes = NULL,
  plot = TRUE,
  da_fdr = 0.1,
  marker_p_val = 0.01
)

Arguments

all_results

A list containing the Milo object, differential abundance results, and design matrix.

samples

Character string specifying the column in metadata representing samples or a covariate.

celltype_var

Character string specifying the column in metadata containing cell type annotations.

celltypes

Character vector specifying the cell types to consider. If NULL, all cell types are considered. Default is NULL.

plot

Logical indicating whether to generate diagnostic plots. Default is TRUE.

da_fdr

Numeric value specifying the FDR threshold for differentially abundant neighborhoods. Default is 0.1.

marker_p_val

Numeric value specifying the p-value threshold for marker gene identification. Default is 0.01.

Value

A vector of marker gene identifiers.

Details

This function identifies marker genes for differentially abundant neighborhoods, optionally focusing on specified cell types, and can generate diagnostic plots.

Examples

# Example usage:
# markers <- find_markers(all_results, samples = "sample_id", celltype_var = "cell_type")