read_adat {SomaDataIO}

Read (Load) SomaLogic ADATs

Description

The parse and load a ⁠*.adat⁠ file as a data.frame-like object into an R workspace environment. The class of the returned object is a soma_adat object.

read.adat() is . For backward compatibility it will likely never go away completely, but you are strongly encouraged to shift your code to use read_adat().

is.soma_adat() checks whether an object is of class soma_adat. See inherits().

Usage

read_adat(file, debug = FALSE, verbose = getOption("verbose"), ...)

read.adat(file, debug = FALSE, verbose = getOption("verbose"), ...)

is.soma_adat(x)

Arguments

file

Character. The elaborated path and file name of the ⁠*.adat⁠ file to be loaded into an R workspace.

debug

Logical. Used for debugging and development of an ADAT that fails to load, particularly out-of-spec, poorly modified, or legacy ADATs.

verbose

Logical. Should the function call be run in verbose mode, printing relevant diagnostic call information to the console.

...

Additional arguments passed ultimately to read.delim(), or additional arguments passed to either other S3 print or summary methods as required by those generics.

x

An R object to test.

Value

A data.frame-like object of class soma_adat consisting of SomaLogic RFU (feature) data and clinical meta data as columns, and samples as rows. Row names are labeled with the unique ID "SlideId_Subarray" concatenation. The sections of the ADAT header (e.g., "Header.Meta", "Col.Meta", ...) are stored as attributes (e.g. attributes(x)$Header.Meta).

Logical. Whether x inherits from class soma_adat.

Author(s)

Stu Field

See Also

read.delim()

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

Examples

# path to *.adat file
# replace with your file path
adat_path <- system.file("extdata", "example_data10.adat",
                         package = "SomaDataIO", mustWork = TRUE)
adat_path

my_adat <- read_adat(adat_path)

is.soma_adat(my_adat)