Scale Transform soma_adat Columns/Rows — transform • SomaDataIO

Scale the i-th row or column of a soma_adat object by the i-th element of a vector. Designed to facilitate linear transformations of only the analyte/RFU entries by scaling the data matrix. If scaling the analytes/RFU (columns), v must have getAnalytes(adat, n = TRUE) elements. If scaling the samples (rows), v must have nrow(_data) elements.

Usage

# S3 method for soma_adat
transform(`_data`, v, dim = 2L, ...)

Arguments

_data: A soma_adat object.
v: A numeric vector of the appropriate length corresponding to dim.
dim: Integer. The dimension to apply elements of v to. 1 = rows; 2 = columns (default).
...: Currently not used but required by the S3 generic.

Value

A modified value of _data with either the rows or columns linearly transformed by v.

Details

Performs the following operations (quickly):

Columns: $$ M_{nxp} = A_{nxp} * diag(v)_{pxp} $$

Rows: $$ M_{nxp} = diag(v)_{nxn} * A_{nxp} $$

Note

This method in intentionally naive, and assumes the user has ordered v to match the columns/rows of _data appropriately. This must be done upstream.

Examples

# simplified example of underlying operations
M <- matrix(1:12, ncol = 4)
M
#>      [,1] [,2] [,3] [,4]
#> [1,]    1    4    7   10
#> [2,]    2    5    8   11
#> [3,]    3    6    9   12

v <- 1:4
M %*% diag(v)    # transform columns
#>      [,1] [,2] [,3] [,4]
#> [1,]    1    8   21   40
#> [2,]    2   10   24   44
#> [3,]    3   12   27   48

v <- 1:3
diag(v) %*% M    # transform rows
#>      [,1] [,2] [,3] [,4]
#> [1,]    1    4    7   10
#> [2,]    4   10   16   22
#> [3,]    9   18   27   36

# dummy ADAT example:
v    <- c(2, 0.5)     # double seq1; half seq2
adat <- data.frame(sample      = paste0("sample_", 1:3),
                   seq.1234.56 = c(1, 2, 3),
                   seq.9999.88 = c(4, 5, 6) * 10)
adat
#>     sample seq.1234.56 seq.9999.88
#> 1 sample_1           1          40
#> 2 sample_2           2          50
#> 3 sample_3           3          60

# `soma_adat` to invoke S3 method dispatch
class(adat) <- c("soma_adat", "data.frame")
trans <- transform(adat, v)
data.frame(trans)
#>     sample seq.1234.56 seq.9999.88
#> 1 sample_1           2          20
#> 2 sample_2           4          25
#> 3 sample_3           6          30

Scale Transform `soma_adat` Columns/Rows