read_adat: 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)

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.

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.

Author

Stu Field

Examples

Run this code

# 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)