getPPI: Generating Protein-Protein Interaction Descriptors

In Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Description

Generating Protein-Protein Interaction Descriptors

Usage

getPPI(protmat1, protmat2, type = c("combine", "tensorprod",
  "entrywise"))

Arguments

protmat1	The first protein descriptor matrix, must have the same ncol with protmat2.
protmat2	The second protein descriptor matrix, must have the same ncol with protmat1.
type	The interaction type, one or more of "combine", "tensorprod", and "entrywise".

Details

This function calculates the protein-protein interaction descriptors by three types of interaction:

• combine - combine the two descriptor matrix, result has (p + p) columns

• tensorprod - calculate column-by-column (pseudo)-tensor product type interactions, result has (p * p) columns

• entrywise - calculate entrywise product and entrywise sum of the two matrices, then combine them, result has (p + p) columns

Value

A matrix containing the protein-protein interaction descriptors

Author(s)

Nan Xiao <https://nanx.me>

See Also

See getCPI for generating compound-protein interaction descriptors.

Examples

x = matrix(1:10, ncol = 2)
y = matrix(5:14, ncol = 2)

getPPI(x, y, type = 'combine')
getPPI(x, y, type = 'tensorprod')
getPPI(x, y, type = 'entrywise')
getPPI(x, y, type = c('combine', 'tensorprod'))
getPPI(x, y, type = c('combine', 'entrywise'))
getPPI(x, y, type = c('entrywise', 'tensorprod'))
getPPI(x, y, type = c('combine', 'entrywise', 'tensorprod'))

Rcpi documentation built on Nov. 8, 2020, 8:23 p.m.