Complexing: Calculate Complex Interaction

In stevexniu/scMatchmaker: Single Cell Matchmaker

Calculate Complex Interaction

Description

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.

Usage

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

## Not run: 
# 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")

## End(Not run)

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