Construct a phip_data object

Creates a fully-validated S3 object that bundles the tidy PhIP-Seq counts (data_long), a peptide-library annotation table, and other metadata. The data itself is validated via validate_phip_data().

Usage

create_data(
  data_long,
  peptide_library = TRUE,
  auto_expand = TRUE,
  materialise_table = TRUE,
  meta = list()
)

Arguments

data_long

A tidy data frame (or tbl_lazy) with one row per peptide_id x sample_id combination. Required.

peptide_library

A data frame with one row per peptide_id and its annotations. If NULL, the package’s current default library is used.

auto_expand

Logical. If TRUE and the input is not already the full Cartesian product of sample_id x peptide_id, the function fills in the missing combinations.

• Columns that are constant within a sample_id (metadata) are duplicated to the newly created rows.

• Measurement columns such as fold_change, exist, raw counts, or any other non-recyclable fields are initialised to 0. The expanded table replaces data_long in place.

materialise_table

Logical. If FALSE (default) the result is registered as a view. If TRUE the result is fully materialised and stored as a physical table, which speeds up repeated queries at the cost of extra memory/disk.

meta

Optional named list of metadata flags to pre-populate the meta slot (rarely needed by users).

Value

An object of class "phip_data".

Examples

## minimal constructor call
tidy_counts <- data.frame(
  sample_id = c("s1", "s1"),
  peptide_id = c("p1", "p2"),
  exist = c(1, 0),
  stringsAsFactors = FALSE
)
pd <- create_data(
  data_long = tidy_counts,
  peptide_library = FALSE,
  materialise_table = FALSE
)
#> [13:45:25] INFO  Constructing <phip_data> object
#>                  -> create_data()
#> [13:45:25] INFO  Validating <phip_data>
#>                  -> validate_phip_data()
#> [13:45:25] INFO  Checking structural requirements (shape & mandatory columns)
#> [13:45:25] INFO  Checking outcome family availability (exist / fold_change /
#>                  raw_counts)
#> [13:45:25] INFO  Checking collisions with reserved names
#>                    - subject_id, sample_id, timepoint, peptide_id, exist,
#>                      fold_change, counts_input, counts_hit
#> [13:45:25] INFO  Ensuring all columns are atomic (no list-cols)
#> [13:45:25] INFO  Checking key uniqueness
#> [13:45:25] INFO  Validating value ranges & types for outcomes
#> [13:45:25] INFO  Assessing sparsity (NA/zero prevalence vs threshold)
#>                    - warn threshold: 50%
#> [13:45:25] INFO  Checking peptide_id coverage against peptide_library
#> [13:45:25] INFO  Checking full grid completeness (peptide * sample)
#> [13:45:25] OK    Counts table is a full peptide * sample grid
#> [13:45:25] OK    Validating <phip_data> - done
#>                  -> elapsed: 0.019s
#> [13:45:25] OK    Constructing <phip_data> object - done
#>                  -> elapsed: 0.02s