Get feature names

Gets and sets feature names (i.e., rownames, usually genes).

Usage

# S4 method for class 'FactorisedExperiment'
names(x) <- value

# S4 method for class 'FactorisedExperiment'
featureNames(x) <- value

# S4 method for class 'FactorisedExperiment'
rownames(x) <- value

# S4 method for class 'ModularExperiment'
names(x) <- value

# S4 method for class 'ModularExperiment'
featureNames(x) <- value

# S4 method for class 'ModularExperiment'
rownames(x) <- value

# S4 method for class 'ReducedExperiment'
featureNames(x)

# S4 method for class 'ReducedExperiment'
names(x) <- value

# S4 method for class 'ReducedExperiment'
rownames(x) <- value

# S4 method for class 'ReducedExperiment'
ROWNAMES(x) <- value

# S4 method for class 'ReducedExperiment'
featureNames(x) <- value

Arguments

x

ReducedExperiment object.

value

New value to replace existing names.

Value

A vector containing the names of the features.

Author

Jack Gisby

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
)

# Methods return equivalent results
stopifnot(all.equal(featureNames(re), rownames(rand_assay_data)))
stopifnot(all.equal(rownames(re), rownames(rand_assay_data)))
stopifnot(all.equal(names(re), rownames(rand_assay_data)))

# We can change the feature name at a particular position
print(paste0("Feature name at position 55: ", featureNames(re)[55]))
#> [1] "Feature name at position 55: gene_55"
featureNames(re)[55] <- "custom_feature_name"
print(paste0("Reduced data at position 55: ", featureNames(re)[55]))
#> [1] "Reduced data at position 55: custom_feature_name"