Differential Interactions

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.

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

if (FALSE) {
object <- Differing(object, interaction1 = "Macrophage|CAF", interaction2 = "Macrophage|Tumor")
}