SomaDataIO-package | R Documentation |
Load and export 'SomaScan' data via the 'Standard BioTools, Inc.' structured text file called an ADAT ('*.adat'). For file format see https://github.com/SomaLogic/SomaLogic-Data/blob/main/README.md. The package also exports auxiliary functions for manipulating, wrangling, and extracting relevant information from an ADAT object once in memory.
Load an ADAT file into the global workspace with a call
to read_adat()
. This function parses the main data
table into a data.frame
object and assigns the remaining data from
the file as object attributes
, i.e. call attributes(adat)
.
Other functions in the package are designed to make extracting,
manipulating, and wrangling data in the newly created soma_adat
object more convenient.
Those familiar with micro-array data analysis and associated packages, e.g.
Biobase, will notice that the feature data (proteins) are arranged as
columns and the samples (arrays) are the rows. This is the
transpose of typical micro-array data. This conflict can be easily solved
using the transpose function, t()
, which is part of the base R
.
In addition, those familiar with the standard ExpressionSet
object,
available from Bioconductor
, might find the functions adat2eSet()
and
pivotExpressionSet()
particularly useful.
Maintainer: Caleb Scheidel calebjscheidel@gmail.com
Authors:
Stu Field stu.g.field@gmail.com (ORCID)
Other contributors:
Standard BioTools, Inc. [copyright holder, funder]
Useful links:
Report bugs at https://github.com/SomaLogic/SomaDataIO/issues
# a listing of all pkg functions
library(help = SomaDataIO)
# the `soma_adat` class
class(example_data)
is.soma_adat(example_data)
# Annotations Lookup Table
anno_tbl <- getAnalyteInfo(example_data)
anno_tbl
# Find all analytes starting with "MMP" in `anno_tbl`
dplyr::filter(anno_tbl, grepl("^MMP", Target))
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