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Scale and Center a Matrix

Source: R/time_series_clustering.R
mscale.Rd

mscale scales and centers each row of a matrix, with options for using mean or median, standard deviation or mean absolute deviation, and censoring extreme values.

Usage

mscale(x, center = TRUE, scale = TRUE, censor = NULL, useMad = FALSE)

Arguments

x

A numeric matrix where rows are features and columns are samples.

center

Logical. If TRUE, the rows are centered by subtracting the mean or median. Default is TRUE.

scale

Logical. If TRUE, the rows are scaled by dividing by the standard deviation or mean absolute deviation. Default is TRUE.

censor

A numeric vector of length one or two for censoring the scaled values. If length one, values are censored symmetrically at positive and negative values. If length two, the first value is the lower limit and the second value is the upper limit. Default is NULL.

useMad

Logical. If TRUE, the mean absolute deviation is used for scaling instead of the standard deviation. Default is FALSE.

Value

A scaled and centered numeric matrix with the same dimensions as the input matrix `x`.

Details

The function allows for flexible scaling and centering of the rows of a matrix:

  • If both center and scale are TRUE, rows are centered and scaled.

  • If only center is TRUE, rows are centered but not scaled.

  • If only scale is TRUE, rows are scaled but not centered.

  • If neither center nor scale is TRUE, the original matrix is returned.

The function can also censor extreme values, either symmetrically or asymmetrically, based on the censor parameter.

Examples

# Create a sample matrix (3 rows by 5 columns)
sample_matrix <- matrix(c(1:15), nrow = 3, byrow = TRUE)

# Scale and center the matrix using the default settings
mscale(sample_matrix, center = TRUE, scale = TRUE)
#>           [,1]       [,2] [,3]      [,4]     [,5]
#> [1,] -1.264911 -0.6324555    0 0.6324555 1.264911
#> [2,] -1.264911 -0.6324555    0 0.6324555 1.264911
#> [3,] -1.264911 -0.6324555    0 0.6324555 1.264911

# Only center the matrix without scaling
mscale(sample_matrix, center = TRUE, scale = FALSE)
#>      [,1] [,2] [,3] [,4] [,5]
#> [1,]   -2   -1    0    1    2
#> [2,]   -2   -1    0    1    2
#> [3,]   -2   -1    0    1    2

# Only scale the matrix without centering
mscale(sample_matrix, center = FALSE, scale = TRUE)
#>           [,1]     [,2]     [,3]     [,4]     [,5]
#> [1,] 0.6324555 1.264911 1.897367 2.529822 3.162278
#> [2,] 3.7947332 4.427189 5.059644 5.692100 6.324555
#> [3,] 6.9570109 7.589466 8.221922 8.854377 9.486833