SomaDataIO (version 6.2.0)

SomaDataIO-package: SomaDataIO: Input/Output 'SomaScan' Data

Description

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.

Author

Maintainer: Caleb Scheidel

Authors:

• Stu Field (ORCID)

Other contributors:

• Standard BioTools, Inc. [copyright holder, funder]

Details

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.

See Also

Useful links:

• https://somalogic.github.io/SomaDataIO/

• https://somalogic.com

• Report bugs at https://github.com/SomaLogic/SomaDataIO/issues

Examples

# 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))