Identify features for gene program discovery.

Identify features for gene program discovery.

findNetworkFeatures(
  object,
  method = c("expr", "hvg", "deviance"),
  n_features = 2000,
  min_pct = 0.5,
  split_var = "seurat_clusters",
  batch_feature = NULL,
  verbose = T
)

Arguments

object

Seurat object

method

Feature selection method.

  • "expr" - Top expressed genes within `split_var` groups, together with variable genes.

  • "hvg" - Highly-variable genes (number specified by `n_features`)

  • "deviance" - Deviant genes (number specified by `n_features`)

n_features

Number of features to use when calculating variable or deviant features. Default is 2000.

min_pct

Minimum expression within spilt_var. Ignored if `method` is not "expr". Default is 0.5.

split_var

Grouping variable to enforce `min_pct` criteria within. Default is 'seurat_clusters'.

batch_feature

Variables to regress out. Ignored if `method` is not "deviance". Default is NULL.

verbose

Show progress. Default is T.

Value

vector of features

See also

runSSN

Author

Nicholas Mikolajewicz