Calculate Complex Interaction

Calculate complex interactions by combining its subunits. Each complex is named by its subunits saperated by semicolon, such as ITGB1:ITGA2. Therefore COL9A2_ITGB1:ITGA2 represents interactions between COL9A2 and ITGB1:ITGA2 complex.

Complexing(
  object,
  subunit_a = c("subunit_a_1", "subunit_a_2", "subunit_a_3"),
  subunit_b = c("subunit_b_1", "subunit_b_2", "subunit_b_3"),
  strength_comb = c("min", "average", "max"),
  pval_comb = c("max", "average", "min")
)

Arguments

object

Matchmaker object.

subunit_a

Column names or indices (of @interactions slot) containing complex subunits information for interaction partner_a. Default is subunit_a_1, subunit_a_2, subunit_a_3.

subunit_b

Column names or indices (of @interactions slot) containing complex subunits information for interaction partner_b. Default is subunit_b_1, subunit_b_2, subunit_b_3.

strength_comb

Method to combine complex interaction strengths from its subunits. Default is min (minimum).

• min, minimum strength of its subunits.

• average, average strength of its subunits.

• max, maximum strength of its subunits.

pval_comb

Method to combine complex interaction p values from its subunits. Default is max (maximum).

• max, maximum p value of its subunits.

• average, average p value of its subunits.

• min, minimum p value of its subunits.

Value

Returns a Matchmaker object.

Examples

if (FALSE) {
# For example, if CellPhoneDB data is used via LoadCellPhoneDB function, 
# the subunits are named as subunit_a_1, subunit_a_2 ...
object <- Complexing(object, strength_comb = "min", pval_comb = "max")
}