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Case study data

Xiaotao Shen (https://www.shenxt.info/)

Created on 2022-03-07 and updated on 2022-03-21

case_study_data.Rmd

MS1 Raw data

The raw data of the case study (MS1, mzML format) is accessible on MetaboLights with MTBLS1122 (HILIC positive), MTBLS1124 (HILIC negative), MTBLS1122 (RPLC positive) and MTBLS1130 (RPLC negative).

MS2 raw data

The raw data of the case study (MS2, mgf format) is accessible here.

Processed data

The processed data (“mass_dataset” class) from the massProcesser package are available here.

Other data

You can also download all the other dataset which are necessary for reproducible analysis for case_study.

  1. data_cleaning

  2. metabolite_annotation

  3. pathway_enrichment

  4. sample_info

  5. Statistical_analysis

Session information 

sessionInfo()
#> R version 4.1.2 (2021-11-01)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur 10.16
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] rstudioapi_0.13   knitr_1.37        magrittr_2.0.2    R6_2.5.1         
#>  [5] ragg_1.2.1        rlang_1.0.1       fastmap_1.1.0     stringr_1.4.0    
#>  [9] tools_4.1.2       xfun_0.29         cli_3.2.0         jquerylib_0.1.4  
#> [13] htmltools_0.5.2   systemfonts_1.0.3 yaml_2.3.4        digest_0.6.29    
#> [17] rprojroot_2.0.2   pkgdown_2.0.2     crayon_1.5.0      textshaping_0.3.6
#> [21] purrr_0.3.4       sass_0.4.0        fs_1.5.2          memoise_2.0.1    
#> [25] cachem_1.0.6      evaluate_0.15     rmarkdown_2.11    stringi_1.7.6    
#> [29] compiler_4.1.2    bslib_0.3.1       desc_1.4.0        jsonlite_1.7.3