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()
.
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
.
See also
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
#> [1] "/Users/runner/work/_temp/Library/SomaDataIO/extdata/example_data10.adat"
my_adat <- read_adat(adat_path)
is.soma_adat(my_adat)
#> [1] TRUE