Load ADAT files as a list

Load a series of ADATs and return a list of soma_adat objects, one for each ADAT file. collapseAdats() concatenates a list of ADATs from loadAdatsAsList(), while maintaining the relevant attribute entries (mainly the HEADER element). This makes writing out the final object possible without the loss of HEADER information.

Usage

loadAdatsAsList(files, collapse = FALSE, verbose = interactive(), ...)

collapseAdats(x)

Arguments

files: A character string of files to load.
collapse: Logical. Should the resulting list of ADATs be collapsed into a single ADAT object?
verbose: Logical. Should the function call be run in verbose mode.
...: Additional arguments passed to read_adat().
x: A list of soma_adat class objects returned from loadAdatsAsList().

Value

A list of ADATs named by files, each a soma_adat object corresponding to an individual file in files. For collapseAdats(), a single, collapsed soma_adat object.

Details

Note 1:

The default behavior is to "vertically bind" (rbind()) on the intersect of the column variables, with unique columns silently dropped.

Note 2:

If "vertically binding" on the column union is desired, use dplyr::bind_rows(), however this results in NAs in non-intersecting columns. For many files with little variable intersection, a sparse RFU-matrix will result (and will likely break ADAT attributes):

adats <- loadAdatsAsList(files)
union_adat <- dplyr::bind_rows(adats, .id = "SourceFile")

Author

Stu Field

Examples

# only 1 file in directory
dir(system.file("extdata", package = "SomaDataIO"))
#> [1] "example_data10.adat"

files <- system.file("extdata", package = "SomaDataIO") |>
  dir(pattern = "[.]adat$", full.names = TRUE) |> rev()

adats <- loadAdatsAsList(files)
class(adats)
#> [1] "list"

# collapse into 1 ADAT
collapsed <- collapseAdats(adats)
class(collapsed)
#> [1] "soma_adat"  "data.frame"

# Alternatively use `collapse = TRUE`
# \donttest{
  loadAdatsAsList(files, collapse = TRUE)
#> ══ SomaScan Data ══════════════════════════════════════════════════════
#>      SomaScan version     V4 (5k)
#>      Signal Space         5k
#>      Attributes intact    ✓
#>      Rows                 10
#>      Columns              5318
#>      Clinical Data        34
#>      Features             5284
#> ── Column Meta ────────────────────────────────────────────────────────
#> ℹ SeqId, SeqIdVersion, SomaId, TargetFullName, Target,
#> ℹ UniProt, EntrezGeneID, EntrezGeneSymbol, Organism, Units,
#> ℹ Type, Dilution, PlateScale_Reference, CalReference,
#> ℹ Cal_Example_Adat_Set001, ColCheck,
#> ℹ CalQcRatio_Example_Adat_Set001_170255, QcReference_170255,
#> ℹ Cal_Example_Adat_Set002,
#> ℹ CalQcRatio_Example_Adat_Set002_170255, Dilution2
#> ── Tibble ─────────────────────────────────────────────────────────────
#> # A tibble: 10 × 5,319
#>    row_names      PlateId  PlateRunDate ScannerID PlatePosition SlideId
#>    <chr>          <chr>    <chr>        <chr>     <chr>           <dbl>
#>  1 258495800012_3 Example… 2020-06-18   SG152144… H9            2.58e11
#>  2 258495800004_7 Example… 2020-06-18   SG152144… H8            2.58e11
#>  3 258495800010_8 Example… 2020-06-18   SG152144… H7            2.58e11
#>  4 258495800003_4 Example… 2020-06-18   SG152144… H6            2.58e11
#>  5 258495800009_4 Example… 2020-06-18   SG152144… H5            2.58e11
#>  6 258495800012_8 Example… 2020-06-18   SG152144… H4            2.58e11
#>  7 258495800001_3 Example… 2020-06-18   SG152144… H3            2.58e11
#>  8 258495800004_8 Example… 2020-06-18   SG152144… H2            2.58e11
#>  9 258495800001_8 Example… 2020-06-18   SG152144… H12           2.58e11
#> 10 258495800004_3 Example… 2020-06-18   SG152144… H11           2.58e11
#> # ℹ 5,313 more variables: Subarray <dbl>, SampleId <chr>,
#> #   SampleType <chr>, PercentDilution <int>, SampleMatrix <chr>,
#> #   Barcode <lgl>, Barcode2d <chr>, SampleName <lgl>,
#> #   SampleNotes <lgl>, AliquotingNotes <lgl>, …
#> ═══════════════════════════════════════════════════════════════════════
# }