Diminished plasma serotonin and taurine levels are a metabolic feature of age-related macular degeneration
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<p>This dataset contains metabolomics data from samples collected from patients with Age-Related Macular Degeneration (AMD) and control participants. The data includes processed metabolomic measurements, clinical data, and genetic risk scores (GRS) for each sample, as well as allele scores for 52 single nucleotide polymorphisms (SNPs) associated with AMD.</p>
<h3>Information about the data:</h3>
<h4>The dataset contains <b>99 samples</b>, which are organized as follows:</h4>
<ul>
<li><strong>Controls</strong> (noAMD): 39 samples</li>
<li><strong>Early / Intermediate AMD</strong> (eAMD): 21 samples</li>
<li><strong>Late AMD</strong> (lAMD): 39 samples</li>
</ul>
One AMD sample (I-AMD 041) and one control sample (I-AMD HC 021) were excluded from the analysis. These samples remain in the dataset but were not included in the analysis due to diagnoses of unrelated disease conditions after sampling that did not meet the study's inclusion criteria.
<h3>Data restrictions:</h3>
<p> Due to hospital data protection policies and privacy regulations, the data and metadata underlying this study are made available under restrictions. Researchers may request access through the PI and data manager. Please fill out the
<a href="https://www.umcutrecht.nl/en/data-request-form-umc-utrecht" target="_blank" rel="noopener">
request form</a> or via de Contact Owner button (top right of this page).</p>
<h3>Information about the uploaded dataset files:</h3>
<p>A complete overview of all data files is described in <a href="https://dataverse.nl/api/access/datafile/607664">README</a>.</p>
<p><b>Go to the Files tab and click on "Change view to Tree" to view the folder structure. </b>
The dataset consists of the following main parts:</p>
<ul>
<li><a href="https://dataverse.nl/api/access/datafile/607634"><b>paper_analysis.Rmd</b></a>, which is used to perform statistical analysis and generate figures and tables for the paper (see also <a href="https://dataverse.nl/api/access/datafile/607665">paper_analysis.html</a>). This RMD file relies on the functions defined in <a href="https://dataverse.nl/api/access/datafile/607630" >00_functions.R</a> from the <b>R</b> folder.</li>
<li>The <b>Data</b> folder, containing both the raw and processed data files, as well as metadata files.</li>
<li>The <b>Output</b> folder, which stores the results of the analysis, including figures, tables, and cached data files.</li>
<li>The <b>R</b> folder, containing the R scripts used for data processing and analysis.</li>
<li>The <b>External Files</b> folder, containing any additional external resources such as figure made in illustrator.</li>
</ul>
<p>All folders have been organized and uploaded in a way that aligns with the structure of an R project. If you download all the files at once, you can directly load the dataset into an R environment, and the folder structure will be preserved, allowing you to use the project seamlessly without any further setup.</p>
<h4>The <b>Metadata</b> folder:</h4>
<p>The metadata for the study consists of clinical and genetic information. The <a href="https://dataverse.nl/api/access/datafile/607649">`clinicaldata.csv`</a> file contains clinical details for all participants, such as sex, age, smoking status, AMD stage, and medication usage. The <a href="https://dataverse.nl/api/access/datafile/607651">`GRS_df.csv`</a> file includes genetic risk scores (GRS-52) and allele scores for 52 SNPs associated with AMD risk. These two files were merged into <a href="https://dataverse.nl/api/access/datafile/607647">`participant_info.csv`</a> using the <a href="https://dataverse.nl/api/access/datafile/607639">`R/01_metadata_processing.R`</a> script, which combined the metadata for analysis.</p>
<h4>The <b>Data</b> folder:</h4>
<p>The raw data for the metabolomics analysis is provided in the <a href="https://dataverse.nl/api/access/datafile/607645">`Results_P-21050.zip`</a> archive, which contains the experimental results. Additionally, the <a href="https://dataverse.nl/api/access/datafile/607626">`Quant_500_Metabolic_Indicators.csv`</a> file provides metabolic indicators used in the analysis, including formulas and identifiers. These raw data files are processed using the <a href="https://dataverse.nl/api/access/datafile/607642">`R/02_data_processing.R`</a> script, which performs preprocessing of the data for further analysis.</p>
<p>The processed data includes multiple versions of the metabolomics data after various processing steps, including normalization, filtering, Box-Cox transformation, and standardization relative to controls. The following files are included:</p>
<ul>
<li><a href="https://dataverse.nl/api/access/datafile/607627">`mdat_wmi_nf.csv`</a>: CSV file with metabolomics data that has been normalized and filtered.</li>
<li><a href="https://dataverse.nl/api/access/datafile/607656">`mdat_wmi_nfb.csv`</a>: CSV file containing metabolomics data with normalization, filtering, and Box-Cox transformation applied.</li>
<li><a href="https://dataverse.nl/api/access/datafile/607657">`mdat_wmi_nfbs.csv`</a>: CSV file with metabolomics data that has undergone normalization, filtering, Box-Cox transformation, and standardization relative to controls.</li>
</ul>
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提供机构：
DataverseNL
创建时间：
2024-09-19
