Analyze communication impact on gene expression — communication

Compute the impact of communication on gene expression using correlation or tree-based methods.

Usage

communication_impact(
  seurat_obj,
  database_name,
  genes,
  keys = NULL,
  signal_type = c("sender", "receiver"),
  method = c("correlation", "partial_correlation", "semipartial_correlation",
    "random_forest", "gradient_boosting"),
  assay = NULL,
  slot = "data",
  n_workers = 1L,
  verbose = TRUE
)

Arguments

seurat_obj

Seurat object with COMMOTR results.

database_name

Database name.

genes

Genes to analyze impact for.

keys

LR pairs or pathways to consider as features.

signal_type

"sender" or "receiver".

method

Impact analysis method:

"correlation": Pearson correlation
"partial_correlation": Partial correlation controlling for total
"semipartial_correlation": Semipartial correlation
"random_forest": Random forest feature importance
"gradient_boosting": Gradient boosting feature importance

assay

Assay to use.

slot

Expression slot.

n_workers

Number of parallel workers.

verbose

Print progress.

Value

Data frame with impact scores for each gene-pathway pair.