getCPI: Generating Interaction Descriptors

In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

Description

Generating Interaction Descriptors

Usage

getCPI(drugmat, protmat, type = c("combine", "tensorprod"))

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

getDDI(DNAmat1, DNAmat2, type = c("combine", "tensorprod", "entrywise"))

getDPI(DNAmat, protmat, type = c("combine", "tensorprod"))

getCCI(drugmat1, drugmat2, type = c("combine", "tensorprod",
  "entrywise"))

getCDI(drugmat, DNAmat, type = c("combine", "tensorprod"))

Arguments

drugmat	The compound descriptor matrix.
protmat	The protein descriptor matrix.
type	The interaction type, one or more of "combine", "tensorprod", and "entrywise".
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.
DNAmat1	The first DNA descriptor matrix, must have the same ncol with DNAmat2.
DNAmat2	The second DNA descriptor matrix, must have the same ncol with DNAmat1.
DNAmat	The DNA descriptor matrix.
drugmat1	The first compound descriptor matrix, must have the same ncol with drugmat2.
drugmat2	The second compound descriptor matrix, must have the same ncol with drugmat1.

Details

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

• combine - combine the two descriptor matrix, result has (p1 + p2) columns

• tensorprod - calculate column-by-column (pseudo)-tensor product type interactions, result has (p1 * p2) 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 interaction descriptors

Author(s)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

Examples

x = matrix(1:10, ncol = 2)
y = matrix(1:15, ncol = 3)
# getCPI 
getCPI(x, y, 'combine')
# getCDI
getCDI(x, y, 'tensorprod')
# getDPI
getDPI(x, y, type = c('combine', 'tensorprod'))
getDPI(x, y, type = c('tensorprod', 'combine'))

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

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

BioMedR documentation built on July 5, 2019, 9:03 a.m.