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Step Function Transformation

Source: R/4-data-preprocessing.R
stepFunctionTranformation.Rd

This function transform input data via a *Step Function*. See stepFunction for further information.

Usage

stepFunctionTranformation(
  x,
  y = c(-1, 0, 1),
  thr = NULL,
  method = c("median", "mean", "mode", "midrange", "trimean", "iqm", "iqr", "mad"),
  by = c("rows", "cols"),
  na.rm = TRUE
)

Arguments

x

a (named) numerical vector or a matrix features-by-samples

y

numerical vector of length 3, the values to use for the piecewise function. The first value is used for the left interval, the second value is used when x == threshold, and the third value is used for the right interval

thr

numerical value, the threshold to use to divide values in x in two intervals

method

character string, indicating the score to be used as threshold. This parameter is only used when thr = NULL or not provided

by

character string, indicating whether to compute the threshold by applying method to rows or columns of x. In the first case, the threshold for the \(i\)-th row is the same across columns. In the second case, the threshold is the same within the same column vector. It is used when x is a matrix

na.rm

logical, whether to remove NA values before the computation of the threshold

Value

A numerical vector or matrix, containing the output of the transformation.

Author

Alessandro Barberis

Examples

#set seed for reproducibility
set.seed(seed = 5381L)

#x is a vector
x = sample(x = -10:10, size = 10)
stepFunctionTranformation(x, thr = 0)
#>  [1] -1 -1  1 -1  1 -1 -1  1  1  0

#x is a matrix
#Define row/col size
nr = 20
nc = 10

#Create input matrix
x = matrix(
 data = stats::runif(n = nr*nc, min = 0, max = 1000),
 nrow = nr,
 ncol = nc,
 dimnames = list(
   paste0("g",seq(nr)),
   paste0("S",seq(nc))
 )
)
#compute
stepFunctionTranformation(x, thr = 500)
#>     S1 S2 S3 S4 S5 S6 S7 S8 S9 S10
#> g1  -1  1 -1 -1 -1 -1  1 -1 -1   1
#> g2   1 -1  1  1 -1  1  1 -1 -1  -1
#> g3   1  1 -1 -1 -1 -1 -1  1  1  -1
#> g4  -1  1 -1  1  1 -1 -1  1 -1  -1
#> g5   1  1  1 -1  1 -1  1 -1  1  -1
#> g6  -1 -1 -1  1 -1  1  1  1 -1   1
#> g7   1  1 -1 -1 -1 -1 -1  1 -1   1
#> g8  -1 -1 -1  1  1 -1 -1  1 -1   1
#> g9  -1  1  1 -1  1  1 -1  1 -1  -1
#> g10 -1 -1  1  1  1 -1  1 -1 -1   1
#> g11 -1  1  1  1 -1  1  1 -1  1   1
#> g12  1  1 -1 -1  1  1  1  1  1  -1
#> g13 -1 -1  1 -1  1  1 -1  1 -1  -1
#> g14 -1 -1 -1 -1  1 -1 -1 -1 -1  -1
#> g15  1  1 -1  1 -1  1  1  1  1   1
#> g16 -1 -1 -1  1  1  1  1  1 -1   1
#> g17  1 -1  1  1  1 -1 -1  1  1   1
#> g18  1  1 -1  1 -1  1 -1  1  1  -1
#> g19  1 -1  1  1  1 -1  1  1 -1   1
#> g20  1  1 -1  1 -1  1 -1  1  1  -1

#use median as threshold
stepFunctionTranformation(x, method = 'median')
#>     S1 S2 S3 S4 S5 S6 S7 S8 S9 S10
#> g1  -1  1 -1  1 -1 -1  1  1 -1   1
#> g2   1 -1  1  1 -1  1  1 -1 -1  -1
#> g3   1  1 -1  1 -1 -1 -1  1  1  -1
#> g4  -1  1 -1  1  1 -1 -1  1  1  -1
#> g5   1  1 -1 -1  1 -1  1 -1  1  -1
#> g6  -1 -1 -1  1 -1  1  1  1 -1   1
#> g7   1  1  1 -1 -1 -1 -1  1 -1   1
#> g8   1 -1 -1  1  1 -1 -1  1 -1   1
#> g9  -1  1  1 -1  1  1 -1  1 -1  -1
#> g10 -1 -1  1  1  1 -1  1 -1 -1   1
#> g11 -1 -1  1  1 -1  1  1 -1 -1   1
#> g12  1  1 -1 -1  1  1 -1  1 -1  -1
#> g13 -1 -1  1 -1  1  1 -1  1  1  -1
#> g14 -1 -1  1  1  1 -1  1 -1  1  -1
#> g15  1 -1 -1  1 -1 -1  1  1 -1   1
#> g16 -1 -1 -1  1  1  1 -1  1 -1   1
#> g17  1 -1 -1  1  1 -1 -1  1 -1   1
#> g18  1  1 -1 -1 -1  1 -1  1  1  -1
#> g19  1 -1 -1  1 -1 -1  1  1 -1   1
#> g20  1  1 -1 -1 -1  1 -1  1  1  -1

#use median as threshold (by columns)
stepFunctionTranformation(x, method = 'median', by = 'cols')
#>     S1 S2 S3 S4 S5 S6 S7 S8 S9 S10
#> g1  -1  1 -1 -1 -1 -1  1 -1 -1   1
#> g2   1 -1  1  1 -1  1  1 -1 -1  -1
#> g3   1  1 -1 -1 -1 -1 -1  1  1  -1
#> g4  -1 -1 -1  1  1 -1 -1 -1 -1  -1
#> g5   1  1  1 -1  1 -1  1 -1  1  -1
#> g6  -1 -1 -1 -1 -1  1  1 -1 -1   1
#> g7   1  1 -1 -1 -1 -1 -1 -1 -1   1
#> g8  -1 -1 -1  1  1 -1 -1 -1 -1   1
#> g9  -1  1  1 -1  1  1 -1  1  1  -1
#> g10 -1 -1  1  1  1 -1  1 -1 -1   1
#> g11 -1  1  1  1 -1  1  1 -1  1   1
#> g12  1  1 -1 -1  1  1  1  1  1  -1
#> g13 -1 -1  1 -1  1  1 -1  1  1  -1
#> g14 -1 -1 -1 -1  1 -1 -1 -1 -1  -1
#> g15  1  1  1  1 -1  1  1  1  1   1
#> g16 -1 -1  1  1  1  1  1  1 -1   1
#> g17  1 -1  1  1  1 -1 -1  1  1   1
#> g18  1  1 -1 -1 -1  1 -1  1  1  -1
#> g19  1 -1  1  1 -1 -1  1  1 -1   1
#> g20  1  1 -1  1 -1  1 -1  1  1  -1