Differing: Differential Interactions

In stevexniu/scMatchmaker: Single Cell Matchmaker

Differential Interactions

Description

Conduct differential interaction analysis based on permutation similar to Matchmaking. To use this feature, save.perm parameter in Matchmaking has to be set to TRUE when running Matchmaking.

Usage

Differing(
  object,
  interaction1,
  interaction2 = NULL,
  diff.thresh = 1,
  p.val.cutoff = 0.05,
  p.adjust.method = "none"
)

Arguments

object	Matchmaker object.
interaction1	Cell-Cell interactions of interests.
interaction2	Cell-Cell interactions to compare against. Default is NULL, all other cell types except the ones in interaction1 will be used.
diff.thresh	Differential interaction strength cutoff, default is 1.
p.val.cutoff	p value cutoff. Default is 0.05
p.adjust.method	p value adjustment method. Default is "none". See details p.adjust.

Value

A data.frame with interaction differences and p values.

Examples

## Not run: 
object <- Differing(object, interaction1 = "Macrophage|CAF", interaction2 = "Macrophage|Tumor")

## End(Not run)

stevexniu/scMatchmaker documentation built on June 2, 2022, 12:35 p.m.