Convert an Experiment to a Tibble

Convert an experiment object to a tibble of "tidy" format. That is, each row is a unique combination of "sample" and "variable", with the observation (the abundance) in the "value" column. Additional columns in the sample and variable information are included. This format is also known as the "long" format.

Usually you don't want all columns in the sample information or variable information tibbles to be included in the output tibble, as this will make the output tibble very "wide". You can specify which columns to include in the output tibble by passing the column names to the sample_cols and var_cols arguments. <data-masking> syntax is used here. By default, all columns are included.

Usage

# S3 method for class 'glyexp_experiment'
as_tibble(
  x,
  sample_cols = tidyselect::everything(),
  var_cols = tidyselect::everything(),
  ...
)

Arguments

x

An experiment().

sample_cols

<data-masking> Columns to include from the sample information tibble.

var_cols

<data-masking> Columns to include from the variable information tibble.

...

Ignored.

Value

A tibble.

Examples

library(tibble)

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

# Convert the experiment to a tibble
as_tibble(toy_exp)
#> # A tibble: 24 × 8
#>    sample group batch variable protein peptide glycan_composition value
#>    <chr>  <chr> <dbl> <chr>    <chr>   <chr>   <chr>              <int>
#>  1 S1     A         1 V1       PRO1    PEP1    H5N2                   1
#>  2 S2     A         2 V1       PRO1    PEP1    H5N2                   5
#>  3 S3     A         1 V1       PRO1    PEP1    H5N2                   9
#>  4 S4     B         2 V1       PRO1    PEP1    H5N2                  13
#>  5 S5     B         1 V1       PRO1    PEP1    H5N2                  17
#>  6 S6     B         2 V1       PRO1    PEP1    H5N2                  21
#>  7 S1     A         1 V2       PRO2    PEP2    H5N2                   2
#>  8 S2     A         2 V2       PRO2    PEP2    H5N2                   6
#>  9 S3     A         1 V2       PRO2    PEP2    H5N2                  10
#> 10 S4     B         2 V2       PRO2    PEP2    H5N2                  14
#> # ℹ 14 more rows

# specify columns to include
as_tibble(toy_exp, sample_cols = group, var_cols = c(protein, peptide))
#> # A tibble: 24 × 6
#>    sample group variable protein peptide value
#>    <chr>  <chr> <chr>    <chr>   <chr>   <int>
#>  1 S1     A     V1       PRO1    PEP1        1
#>  2 S2     A     V1       PRO1    PEP1        5
#>  3 S3     A     V1       PRO1    PEP1        9
#>  4 S4     B     V1       PRO1    PEP1       13
#>  5 S5     B     V1       PRO1    PEP1       17
#>  6 S6     B     V1       PRO1    PEP1       21
#>  7 S1     A     V2       PRO2    PEP2        2
#>  8 S2     A     V2       PRO2    PEP2        6
#>  9 S3     A     V2       PRO2    PEP2       10
#> 10 S4     B     V2       PRO2    PEP2       14
#> # ℹ 14 more rows