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.
There is a version available on CRAN.
install.packages("MetAlyzer")For the latest version install from GitHub
library(devtools)
install_github("nilsmechtel/MetAlyzer")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.
This is an extract from one of the provided example data sets.
> metalyzer <- MetAlyzer_dataset(file_path = extraction_data())
> show(metalyzer)
-------------------------------------
File name: extraction_data.xlsx
Sheet: 1
File path: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/MetAlyzer/extdata
Metabolites: 862
Classes: 24
Including metabolism indicators: TRUE
Number of samples: 74
Columns meta data: "Plate Bar Code"; "Sample Bar Code"; "Sample Type"; "Sample Description"; "Tissue"; "Sample Volume"; "Measurement Time"
Aggregated data available: FALSE
-------------------------------------> na_metabolites <- summariseConcValues(metalyzer)
-------------------------------------
Quantiles:
0% 25% 50% 75% 100%
0.000 0.028 1.960 22.700 288149.000
NAs: 4941 (7.96%)
-------------------------------------> status_list <- summariseQuantData(metalyzer)
-------------------------------------
Valid: 24056 (38.76%)
LOQ: 5790 (9.33%)
LOD: 20577 (33.15%)
Invalid: 11641 (18.76%)
NAs: 0 (0%)
-------------------------------------For further filtering, statistical analysis and plotting, the data can be reformatted and aggregated into a tibble data frame.
> renameMetaData(metalyzer, Method = `Sample Description`)
> filterMetaData(metalyzer, !is.na(Tissue))
> aggregated_data <- aggregateData(metalyzer, Tissue, Method)
> aggregated_data
# A tibble: 62,064 × 8
# Groups: Tissue, Method, Metabolite [20,688]
ID Tissue Method Metabolite Class Concentration Status Valid_Replicates
<fct> <fct> <fct> <fct> <fct> <dbl> <fct> <lgl>
1 9 Drosophi… 1 C0 Acyl… 203 Valid TRUE
2 10 Drosophi… 1 C0 Acyl… 86.8 Valid TRUE
3 11 Drosophi… 1 C0 Acyl… 246 Valid TRUE
4 9 Drosophi… 1 C2 Acyl… 29.5 Valid TRUE
5 10 Drosophi… 1 C2 Acyl… 15.8 Valid TRUE
6 11 Drosophi… 1 C2 Acyl… 34.6 Valid TRUE
7 9 Drosophi… 1 C3 Acyl… 39.2 Valid TRUE
8 10 Drosophi… 1 C3 Acyl… 9.29 Valid TRUE
9 11 Drosophi… 1 C3 Acyl… 49.9 Valid TRUE
10 9 Drosophi… 1 C3-DC (C4… Acyl… 0.057 LOD FALSE
# ℹ 62,054 more rows
# ℹ Use `print(n = ...)` to see more rows
For a comprehensive tutorial, please check out the vignette (<Link_to_User_Manual>).