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Description

Read and Analyze 'MetIDQ™' Software Output Files.

The 'MetAlyzer' S4 object provides methods to read and reformat metabolomics data for convenient data handling, statistics and downstream analysis. The resulting format corresponds to input data of the Shiny app 'MetaboExtract' (<https://www.metaboextract.shiny.dkfz.de/MetaboExtract/>).

MetAlyzer

R-CMD-check license metacran downloads

An R Package to read and analyze MetIDQ™ output

The package provides methods to read output files from the MetIDQ™ software into R. Metabolomics data is read and reformatted into an S4 object for convenient data handling, statistics and downstream analysis.

Install

There is a version available on CRAN.

install.packages("MetAlyzer")

For the latest version install from GitHub

library(devtools)
install_github("nilsmechtel/MetAlyzer")

Quickstart

The package takes metabolomic measurements and the quantification status (e.g. "Valid", "LOQ", "LOD") as ".xlsx" files generated from the MetIDQ™ software. Additionally, meta data for each sample can be provided for further analysis.

MetAlyzer

This is an extract from one of the provided example data sets. Example_Data

Create MetAlyzer object:

> metalyzer_se <- MetAlyzer_dataset(file_path = extraction_data())


 _____ ______   _______  _________  ________  ___           ___    ___ ________  _______   ________
|\   _ \  _   \|\  ___ \|\___   ___\\   __  \|\  \         |\  \  /  /|\_____  \|\  ___ \ |\   __  \
\ \  \\\__\ \  \ \   __/\|___ \  \_\ \  \|\  \ \  \        \ \  \/  / /\|___/  /\ \   __/|\ \  \|\  \
 \ \  \\|__| \  \ \  \_|/__  \ \  \ \ \   __  \ \  \        \ \    / /     /  / /\ \  \_|/_\ \   _  _\
  \ \  \    \ \  \ \  \_|\ \  \ \  \ \ \  \ \  \ \  \____    \/   / /     /  /_/__\ \  \_|\ \ \  \\  \| 
   \ \__\    \ \__\ \_______\  \ \__\ \ \__\ \__\ \_______\__/   / /     |\________\ \_______\ \__\\ _\ 
    \|__|     \|__|\|_______|   \|__|  \|__|\|__|\|_______|\____/ /       \|_______|\|_______|\|__|\|__|
                                                          \|____|/


Info: Reading color code "FFFFCCCC" as "#FFCCCC"
Info: Reading color code "FF00CD66" as "#00CD66"
Info: Reading color code "FF6A5ACD" as "#6A5ACD"
Info: Reading color code "FF87CEEB" as "#87CEEB"
Info: Reading color code "FFFFFFCC" as "#FFFFCC"

Measured concentration values:
------------------------------
        0%        25%        50%        75%       100% 
     0.000      0.017      1.760     21.200 288149.000 

NAs: 5348 (8.38%)
Note: 'Metabolism Indicators' are frequently NA!

Measured quantification status:
-------------------------------
Valid: 24095 (37.77%)
LOQ: 5799 (9.09%)
LOD: 21789 (34.16%)
Invalid: 12105 (18.98%)
NAs: 0 (0%)

Downstream analysis:

For further filtering, statistical analysis and plotting, the data is reformatted and aggregated into a tibble data frame.

> aggregatedData(metalyzer_se)
# A tibble: 63,788 × 5
# Groups:   Metabolite [862]
   ID    Metabolite Class          Concentration Status
   <fct> <fct>      <fct>                  <dbl> <fct> 
 1 9     C0         Acylcarnitines         203   Valid 
 2 10    C0         Acylcarnitines          86.8 Valid 
 3 11    C0         Acylcarnitines         246   Valid 
 4 12    C0         Acylcarnitines         198   Valid 
 5 13    C0         Acylcarnitines         369   Valid 
 6 14    C0         Acylcarnitines         127   Valid 
 7 15    C0         Acylcarnitines          36.1 Valid 
 8 16    C0         Acylcarnitines          40.7 Valid 
 9 17    C0         Acylcarnitines         189   Valid 
10 18    C0         Acylcarnitines          16.1 LOD   
# ℹ 63,778 more rows
# ℹ Use `print(n = ...)` to see more rows

Detailed instructions

For a comprehensive tutorial, please check out the MetAlyzer User Guide.

Metadata

Version

1.0.0

License

Unknown

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