Apply a function to a list of similarities

Function to join list of similarities by a function provided by the user.

Usage

similarities(sim, func, ...)

Arguments

sim

list of similarities to be joined. All similarities must have the same dimensions. The genes are assumed to be in the same order for all the matrices.

func

function to perform on those similarities: prod, sum... It should accept as many arguments as similarities matrices are provided, and should use numbers.

...

Other arguments passed to the function func. Usually na.rm or similar.

Value

A matrix of the size of the similarities

Note

It doesn't check that the columns and rows of the matrices are in the same order or are the same.

See also

weighted() for functions that can be used, and addSimilarities() for a wrapper to one of them

Author

Lluís Revilla

Examples

set.seed(100)
a <- seq2mat(LETTERS[1:5], rnorm(10))
b <- seq2mat(LETTERS[1:5], seq(from = 0.1, to = 1, by = 0.1))
sim <- list(b, a)
similarities(sim, weighted.prod, c(0.5, 0.5))
#>              A            B            C           D           E
#> A  0.250000000 -0.012554809  0.006576558  0.08867848 -0.10181337
#> B -0.012554809  0.250000000 -0.005918782  0.01462141  0.14290654
#> C  0.006576558 -0.005918782  0.250000000  0.04779451 -0.18568337
#> D  0.088678481  0.014621409  0.047794513  0.25000000 -0.08996553
#> E -0.101813370  0.142906542 -0.185683371 -0.08996553  0.25000000
# Note the differences in the sign of some values
similarities(sim, weighted.sum, c(0.5, 0.5))
#>            A          B          C          D          E
#> A  1.0000000 -0.3010962  0.1657656  0.6433924 -0.6408953
#> B -0.3010962  1.0000000 -0.1894585  0.3084856  0.7572664
#> C  0.1657656 -0.1894585  1.0000000  0.4593150 -0.8626297
#> D  0.6433924  0.3084856  0.4593150  1.0000000 -0.6799311
#> E -0.6408953  0.7572664 -0.8626297 -0.6799311  1.0000000