---
title: "Glossary"
output: 
  bookdown::html_document2:
    base_format: rmarkdown::html_vignette
    toc: true
    number_sections: true
    always_allow_html: yes
pkgdown: 
    as_is: true
bibliography: hadex2_docs.bib
vignette: >
  %\VignetteIndexEntry{Glossary}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# Variables

Variable names are used in the package consequently. Below are definitions of the terms. 

## Time points of measurement

time_t - chosen time point of measurement.

time_0 - minimal exchange control time point of measurement.

time_100 - maximal exchange control time point of measurement.

## Deuterium uptake values

deut_uptake -	deuterium uptake [Da].

err_deut_uptake -	error associated with deuterium uptake [Da].

frac_deut_uptake - fractional deuterium uptake [%].

err_frac_deut_uptake - error associated with fractional deuterium uptake [%].

theo_deut_uptake - theoretical deuterium uptake [Da].

err_theo_deut_uptake - error associated with theoreti.cal deuterium uptake [Da].

theo_frac_deut_uptake - theoretical fractional deuterium uptake [%].

err_theo_frac_deut_uptake - error associated with theoretical fractional deuterium uptake [%].

## Experimental conditions

deut_part - deuterium percentage in solution used in experiment, from range [0, 1].




<!-- # Object hdx_data -->

<!-- In the package, the input data is transformed into hdx_data object. The object inherits the data frame properties and has multiple necessary attributes. -->

<!-- ## Main data frame -->

<!-- Protein - character, protein name. May have different values. -->

<!-- Start - integer, start position of the peptide in the protein sequence. -->

<!-- End - integer, end position of the peptide in the protein sequence. -->

<!-- Sequence - character, peptide name.  -->

<!-- MaxUptake - numerical, maximal possible uptake value, based on the peptide sequence. -->

<!-- MHP - numerical, monoisotopic mass of the peptide, based on the peptide sequence [Da]. -->

<!-- State - character, biological state. -->

<!-- Exposure - numerical, time point of the measurement [min]. -->

<!-- File - character, the raw data filename. -->

<!-- z - integer, the charge value. -->

<!-- Inten - numerical, peak intensity. -->

<!-- Center - numerical, geometric centroid value of measured isotopic envelope. -->


<!-- ## Attributes -->

<!-- source - character, indicator of the data source (e.g. DynamX3.0). -->

<!-- has_modification - logical, indicator of the modification presence. The modification information is preserved in the state value. -->
