Retrieves the reduced data matrix, with samples as rows and reduced components as columns. Setter method can be used to replace or modify all or part of the matrix.
Usage
# S4 method for class 'ReducedExperiment'
reduced(object, scale_reduced = FALSE, center_reduced = FALSE)
# S4 method for class 'ReducedExperiment'
reduced(object) <- valueArguments
- object
An object that inherits from ReducedExperiment.
- scale_reduced
If
TRUE, data will be scaled column-wise to have a standard deviation of 0.- center_reduced
If
TRUE, data will be centered column-wise to have a mean of 0.- value
New value to replace existing reduced data matrix.
Value
A matrix with samples/observations as rows and columns referring to the dimensionally-reduced components.
Examples
# Create randomised data with the following dimensions
i <- 300 # Number of features
j <- 100 # Number of samples
k <- 10 # Number of factors
rand_assay_data <- ReducedExperiment:::.makeRandomData(i, j, "gene", "sample")
rand_reduced_data <- ReducedExperiment:::.makeRandomData(j, k, "sample", "component")
re <- ReducedExperiment(
assays = list("normal" = rand_assay_data),
reduced = rand_reduced_data
)
stopifnot(all.equal(reduced(re), rand_reduced_data))
print(paste0("Reduced data at position (2, 2): ", reduced(re)[2, 2]))
#> [1] "Reduced data at position (2, 2): -0.330539477488848"
reduced(re)[2, 2] <- 5
print(paste0("Reduced data at position (2, 2): ", reduced(re)[2, 2]))
#> [1] "Reduced data at position (2, 2): 5"