---
title: "Introduction to SomaDataIO"
output:
  rmarkdown::html_vignette:
    fig_caption: yes
vignette: >
  %\VignetteIndexEntry{Introduction to SomaDataIO}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  echo = TRUE,
  collapse = TRUE,
  comment = "#>"
)
```


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](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.
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](https://dplyr.tidyverse.org) and [tidyr](https://tidyr.tidyverse.org) 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'](https://somalogic.github.io/SomaDataIO/articles/tips-loading-and-wrangling.html)

* 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](https://somalogic.github.io/SomaDataIO/articles/stat-two-group-comparison.html)

- Multi-group comparison (e.g. differential expression) via ANOVA
  + see `stats::aov()`
  + see workflow: [ANOVA Three-Group Analysis](https://somalogic.github.io/SomaDataIO/articles/stat-three-group-analysis-anova.html)

- Binary classification
  + see `stats::glm()`
  + see workflow: [Binary Classification](https://somalogic.github.io/SomaDataIO/articles/stat-binary-classification.html)

- Linear regression
  + see `stats::lm()`
  + see workflow: [Linear Regression](https://somalogic.github.io/SomaDataIO/articles/stat-linear-regression.html)

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™

Copyright © 2024 SomaLogic Operating Co., Inc.

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.