Skip to contents

Identify and Annotate Shared Top Features Across Integration Factors

Source: R/run_factor_overlap.R
run_factor_overlap.Rd

Identifies top features shared across factors based on integration method. For MOFA/MCIA, takes intersection across factors. For DIABLO/RGCCA, takes features recurring in ≥2 block-specific components.

Usage

run_factor_overlap(
  expomicset,
  robust = TRUE,
  stability_score = NULL,
  score_col = "stability_score",
  pval_thresh = 0.05,
  logfc_thresh = log2(1.5),
  pval_col = "padj",
  logfc_col = "logFC",
  action = "add"
)

Arguments

expomicset

A MultiAssayExperiment with integration results and top factor features.

robust

Logical; if TRUE, uses sensitivity score. Otherwise, uses DEG thresholds.

stability_score

Optional numeric threshold (overrides default from metadata).

score_col

Column name for sensitivity score. Default is "stability_score".

pval_thresh

DEG p-value threshold (if robust = FALSE). Default is 0.05.

logfc_thresh

DEG logFC threshold (if robust = FALSE). Default is log2(1.5).

pval_col

Column name for p-value. Default is "padj".

logfc_col

Column name for logFC. Default is "logFC".

action

"add" to return modified object, "get" to return data.frame.

Value

Modified MultiAssayExperiment or data.frame of shared top features.