Introduction to SomaDataIO

This document accompanies the SomaDataIO R package, which loads and exports ‘SomaScan’ data via the Standard BioTools, Inc. structured text file called an ADAT (*.adat). For file format see here. The package also exports auxiliary functions for manipulating, wrangling, and extracting relevant information from an ADAT object once in memory. Basic familiarity with the R environment is assumed, as is the ability to install contributed packages from the Comprehensive R Archive Network (CRAN).

Main Features (I/O)

Loading data (Import)
- parse and import a *.adat text file into an R session as a soma_adat object.
Wrangling data (manipulation)
- subset, reorder, and list various fields of a soma_adat object.
- ?SeqId analyte (feature) matching.
- dplyr and tidyr verb S3 methods for the soma_adat class.
- ?rownames helpers that do not break soma_adat attributes.
- please see the article Loading and Wrangling ‘SomaScan’
Exporting data (Output)
- write out a soma_adat object as a *.adat text file.

Workflows and Analysis

This section will become more fleshed out in future versions of SomaDataIO. In the meantime, below are 4 examples of typical primary statistical analyses that are commonly performed on ‘SomaScan’ data:

Two-group comparison (e.g. differential expression) via t-test
- see stats::t.test()
- see workflow: Two-Group Comparison
Multi-group comparison (e.g. differential expression) via ANOVA
- see stats::aov()
- see workflow: ANOVA Three-Group Analysis
Binary classification
- see stats::glm()
- see workflow: Binary Classification
Linear regression
- see stats::lm()
- see workflow: Linear Regression

Note that, in an effort to reduce package size and dependencies, these articles and workflows are only accessible via the SomaDataIO pkgdown website, and are not included with the installed package.

MIT LICENSE

SomaDataIO™

Permission is hereby granted, free of charge, to any person obtaining a copy of the SomaDataIO software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sub-license, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions outlined below. Further, SomaDataIO and SomaLogic are trademarks owned by Standard BioTools, Inc. No license is hereby granted to these trademarks other than for purposes of identifying the origin or source of the Software.

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

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