Run Complete scMetaLink Analysis

One-step function to run the complete metabolite-mediated cell communication analysis pipeline

runScMetaLink(
  expression_data,
  cell_meta,
  cell_type_column = "cell_type",
  method = "combined",
  min_cells = 10,
  min_pct = 0.1,
  n_permutations = 1000,
  pvalue_threshold = 0.05,
  n_cores = 1,
  verbose = TRUE
)

Arguments

expression_data

A matrix or sparse matrix of normalized expression

cell_meta

A data.frame with cell metadata

cell_type_column

Character. Column name for cell type annotations

method

Character. Expression scoring method: "mean", "proportion", "combined"

min_cells

Integer. Minimum cells per cell type

min_pct

Numeric. Minimum percentage of expressing cells (0-1)

n_permutations

Integer. Number of permutations for significance testing

pvalue_threshold

Numeric. P-value threshold for significance

n_cores

Integer. Number of cores for parallel computing

verbose

Logical. Print progress messages

Value

A scMetaLink object with all analysis completed

Details

This function runs the complete scMetaLink pipeline:

1. Create scMetaLink object from expression data

2. Infer metabolite production potential (MPP)

3. Infer metabolite sensing capability (MSC)

4. Compute cell-cell communication scores

5. Perform permutation-based significance testing

6. Filter significant interactions

7. Aggregate by pathway

Examples

# \donttest{
# Run complete analysis
result <- runScMetaLink(
  expression_data = expr_matrix,
  cell_meta = cell_metadata,
  cell_type_column = "cell_type",
  n_permutations = 1000
)
#> === Step 1/6: Creating scMetaLink object ===
#> Error: object 'expr_matrix' not found

# View significant interactions
sig <- getSignificantInteractions(result)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'getSignificantInteractions': object 'result' not found
head(sig)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'head': object 'sig' not found
# }