profile_multiclusters_DEG — profile_multiclusters

Profile-Specific Differential Expression Across Multiple Clusters

Usage

profile_multiclusters_DEG(
  profile,
  exprs,
  cell_meta,
  cell_profile_prob,
  clusters = NULL,
  cluster_col = "cluster",
  pseudotime_col = "cell_t",
  mass_thresh = 100
)

Arguments

profile: Character. Profile name or index to test.
exprs: A gene expression matrix (genes × cells).
cell_meta: A data frame of cell-level metadata (includes pseudotime and cluster labels).
cell_profile_prob: Matrix of soft profile probabilities (cells × profiles).
clusters: Optional. A vector of cluster names to test. If `NULL`, all clusters are used.
cluster_col: Name of the cluster label column in `cell_meta` (default: `"cluster"`).
pseudotime_col: Name of the pseudotime column in `cell_meta` (default: `"cell_t"`).
mass_thresh: Minimum profile mass in a cluster required to perform DE test (default: 100).

Value

A named list of DE test results, one for each qualifying cluster.

Details

Applies `profile_cluster_DEG()` to a set of clusters to identify genes associated with a specific profile across the transcriptional landscape. Skips clusters where the profile mass is below a threshold.

Examples

res_list <- profile_multiclusters_DEG("P1", exprs, cell_meta, cell_profile_prob)
#> Error in as.matrix(cell_profile_prob): object 'cell_profile_prob' not found
names(res_list)
#> Error in eval(expr, envir, enclos): object 'res_list' not found