Calculate feature co-dependency index

Calculate feature co-dependency index (CDI).

findCDIMarkers(
  object,
  features.x = NULL,
  features.y = rownames(object),
  ncell.subset = 5000,
  geosketch.subset = F,
  assay = DefaultAssay(object),
  slot = "data",
  n.workers = 1,
  verbose = T
)

Arguments

object

Seurat object

features.x

feature or meta feature. CDI between features.x and features.y are computed.

features.y

feature or meta feature. CDI between features.x and features.y are computed.

ncell.subset

max number of cells to run analysis on. Default is 5000. Computationally intensive for larger datasets.

geosketch.subset

Use GeoSketch method to subsample scRNA-seq data while preserving rare cell states (https://doi.org/10.1016/j.cels.2019.05.003). Logical, T or F (Default F). Recommended if cell type representation is imbalanced.

assay

Assay to run CDI scoring on. Default is DefaultAssay(object).

slot

slot to run CDI scoring on. Default is data.

n.workers

number of workers for parallel implementation. Default is 1 (no parallel).

verbose

print progress. Default is T.

Value

data.frame with CDI scores.

See also

binom.test

Author

Nicholas Mikolajewicz