Generating Protein-Protein Interaction Descriptors

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".

Value

A matrix containing the protein-protein interaction descriptors

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

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')
#>      [,1] [,2] [,3] [,4]
#> [1,]    1    6    5   10
#> [2,]    2    7    6   11
#> [3,]    3    8    7   12
#> [4,]    4    9    8   13
#> [5,]    5   10    9   14
getPPI(x, y, type = 'tensorprod')
#>      [,1] [,2] [,3] [,4]
#> [1,]    5   30   10   60
#> [2,]   12   42   22   77
#> [3,]   21   56   36   96
#> [4,]   32   72   52  117
#> [5,]   45   90   70  140
getPPI(x, y, type = 'entrywise')
#>      [,1] [,2] [,3] [,4]
#> [1,]    5   60    6   16
#> [2,]   12   77    8   18
#> [3,]   21   96   10   20
#> [4,]   32  117   12   22
#> [5,]   45  140   14   24
getPPI(x, y, type = c('combine', 'tensorprod'))
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
#> [1,]    1    6    5   10    5   30   10   60
#> [2,]    2    7    6   11   12   42   22   77
#> [3,]    3    8    7   12   21   56   36   96
#> [4,]    4    9    8   13   32   72   52  117
#> [5,]    5   10    9   14   45   90   70  140
getPPI(x, y, type = c('combine', 'entrywise'))
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
#> [1,]    1    6    5   10    5   60    6   16
#> [2,]    2    7    6   11   12   77    8   18
#> [3,]    3    8    7   12   21   96   10   20
#> [4,]    4    9    8   13   32  117   12   22
#> [5,]    5   10    9   14   45  140   14   24
getPPI(x, y, type = c('entrywise', 'tensorprod'))
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
#> [1,]    5   30   10   60    5   60    6   16
#> [2,]   12   42   22   77   12   77    8   18
#> [3,]   21   56   36   96   21   96   10   20
#> [4,]   32   72   52  117   32  117   12   22
#> [5,]   45   90   70  140   45  140   14   24
getPPI(x, y, type = c('combine', 'entrywise', 'tensorprod'))
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
#> [1,]    1    6    5   10    5   30   10   60    5    60     6    16
#> [2,]    2    7    6   11   12   42   22   77   12    77     8    18
#> [3,]    3    8    7   12   21   56   36   96   21    96    10    20
#> [4,]    4    9    8   13   32   72   52  117   32   117    12    22
#> [5,]    5   10    9   14   45   90   70  140   45   140    14    24