loadAdatsAsList: Load ADAT files as a list

In SomaDataIO: Input/Output 'SomaScan' Data

Load ADAT files as a list

Description

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().

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")

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.

Author(s)

Stu Field

See Also

read_adat()

Other IO: parseHeader(), read_adat(), soma_adat, write_adat()

Examples

# only 1 file in directory
dir(system.file("extdata", package = "SomaDataIO"))

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

adats <- loadAdatsAsList(files)
class(adats)

# collapse into 1 ADAT
collapsed <- collapseAdats(adats)
class(collapsed)

# Alternatively use `collapse = TRUE`

  loadAdatsAsList(files, collapse = TRUE)

SomaDataIO documentation built on April 4, 2025, 2:14 a.m.