Introduction to SomaDataIO

This document accompanies the SomaDataIO R package, which loads and exports ‘SomaScan’ data via the SomaLogic Operating Co., 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 vignette vignette("tips-loading-and-wrangling", package = "SomaDataIO")
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 vignette vignette("stat-two-group-comparison", package = "SomaDataIO")
Multi-group comparison (e.g. differential expression) via ANOVA
- see stats::aov()
- see vignette vignette("stat-three-group-analysis-anova", package = "SomaDataIO")
Binary classification
- see stats::glm()
- see vignette vignette("stat-binary-classification", package = "SomaDataIO")
Linear regression
- see stats::lm()
- see vignette vignette("stat-linear-regression", package = "SomaDataIO")

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 SomaLogic Operating Co., 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.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDER(S) BE LIABLE FOR ANY CLAIM, DAMAGES, WHETHER DIRECT OR INDIRECT, OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.