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Compare Cell-Cell Communication Between Conditions

Source: R/diff_edges.R
DiffEdges.Rd

Identify changes in ligand-receptor mediated communication between two conditions (e.g., control vs treatment, healthy vs disease).

Usage

DiffEdges(reference, target, log2fc_threshold = 1, verbose = TRUE)

Arguments

reference

NOVAResult object for the reference condition (e.g., control)

target

NOVAResult object for the target condition (e.g., treatment)

log2fc_threshold

Log2 fold change threshold for calling significant changes

verbose

Print progress messages

Value

A list of class "NOVADiffResult" containing:

  • all_edges: All edges with differential statistics

  • appeared: Edges only in target

  • disappeared: Edges only in reference

  • up: Up-regulated edges

  • down: Down-regulated edges

  • stable: Unchanged edges

  • clusters: Cluster size comparison

  • parameters: Analysis parameters

Details

The function merges edges from both conditions and computes:

  • Fold change: target_weight / reference_weight

  • Log2 fold change: log2(fold_change)

  • Delta: target_weight - reference_weight

Edges are classified as:

  • Appeared: Only detected in target (reference weight = 0)

  • Disappeared: Only detected in reference (target weight = 0)

  • Up: log2FC > threshold

  • Down: log2FC < -threshold

  • Stable: |log2FC| <= threshold

Examples

if (FALSE) { # \dontrun{
# Compare two conditions
diff <- DiffEdges(ctrl_result, treat_result)

# View results
print(diff)
summary(diff)
} # }