Skip to contents

Subsetting experiments

sub-.glyexp_experiment.Rd

Getting a subset of an experiment object. Subsetting is first done on the expression matrix, then the sample information and variable information tibbles are filtered and ordered accordingly.

Syntax for [ is similar to subsetting a matrix, with some differences:

  • Both row and column indices are required, i.e. exp[i] is not allowed, but exp[i, ] and exp[, j] are allowed.

  • drop argument is not supported. Subsetting an experiment always returns an new experiment, even if it has only one sample or one variable.

  • Renaming the subsetted experiment is no longer supported.

Assigning to a subset of an experiment is not allowed, i.e., exp[1, 1[ <- 0 will raise an error. You can create a new experiment with new data if needed.

Usage

# S3 method for class 'glyexp_experiment'
x[i, j, ...]

# S3 method for class 'glyexp_experiment'
x[i, j, ...] <- value

Arguments

x

An experiment().

i, j

Row (variable) and column (sample) indices to subset.

...

Ignored.

value

Ignored.

Value

An experiment() object.

Examples

# Create a toy experiment for demonstration
exp <- toy_experiment()

# Subsetting single samples
exp[, "S1"]
#> 
#> ── Experiment ──────────────────────────────────────────────────────────────────
#> ℹ Expression matrix: 1 samples, 4 variables
#> ℹ Sample information fields: group and batch
#> ℹ Variable information fields: protein, peptide, and glycan_composition
exp[, 1]
#> 
#> ── Experiment ──────────────────────────────────────────────────────────────────
#> ℹ Expression matrix: 1 samples, 4 variables
#> ℹ Sample information fields: group and batch
#> ℹ Variable information fields: protein, peptide, and glycan_composition

# Subsetting single variables
exp["V1", ]
#> 
#> ── Experiment ──────────────────────────────────────────────────────────────────
#> ℹ Expression matrix: 6 samples, 1 variables
#> ℹ Sample information fields: group and batch
#> ℹ Variable information fields: protein, peptide, and glycan_composition
exp[1, ]
#> 
#> ── Experiment ──────────────────────────────────────────────────────────────────
#> ℹ Expression matrix: 6 samples, 1 variables
#> ℹ Sample information fields: group and batch
#> ℹ Variable information fields: protein, peptide, and glycan_composition

# Subsetting multiple samples and variables
exp[c("V1", "V2"), c("S2", "S3")]
#> 
#> ── Experiment ──────────────────────────────────────────────────────────────────
#> ℹ Expression matrix: 2 samples, 2 variables
#> ℹ Sample information fields: group and batch
#> ℹ Variable information fields: protein, peptide, and glycan_composition
exp[c(1, 2), c(2, 3)]
#> 
#> ── Experiment ──────────────────────────────────────────────────────────────────
#> ℹ Expression matrix: 2 samples, 2 variables
#> ℹ Sample information fields: group and batch
#> ℹ Variable information fields: protein, peptide, and glycan_composition

# Create a copy
exp[, ]
#> 
#> ── Experiment ──────────────────────────────────────────────────────────────────
#> ℹ Expression matrix: 6 samples, 4 variables
#> ℹ Sample information fields: group and batch
#> ℹ Variable information fields: protein, peptide, and glycan_composition