1 Installation

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ptairData")

2 Description

This package contains two volatolomics raw datasets acquired with a Proton-Transfer-Reaction Time-of-Flight mass spectrometer (PTR-TOF-MS; Ionicon Analytik GmbH, Innsbruck, Austria). They are stored in two subfolders:

  • exhaledAir: Exhaled air from two healthy individuals, three acquisitions per individual on distinct days [6 files in total], with two expirations per acquisition and Buffered end-tidal (BET) sampling Herbig et al, 2008)

  • mycobacteria: cell culture headspace: two replicates from two species and one control (culture medium only) [6 files]

3 Format

The files are in the open Hierarchical Data Format (HDF5). To limit the size of the data and speed up the analysis in demo examples, the raw data are truncated in the m/z dimension within the range \([20.4, 21.6] \cup [50, 150]\) for individuals, and \([20.4, 21.6] \cup [56.4, 90.6]\) for mycobacteria.

4 Processing

The ptairMS package (also available on Bioconductor) is devoted to the processing of PTR-TOF-MS data.

5 Session info

sessionInfo()
#> R version 4.1.1 (2021-08-10)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.3 LTS
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#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
#> LAPACK: /home/biocbuild/bbs-3.14-bioc/R/lib/libRlapack.so
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_GB              LC_COLLATE=C              
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
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#> other attached packages:
#> [1] BiocStyle_2.22.0
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#> loaded via a namespace (and not attached):
#>  [1] bookdown_0.24       digest_0.6.28       R6_2.5.1           
#>  [4] jsonlite_1.7.2      magrittr_2.0.1      evaluate_0.14      
#>  [7] stringi_1.7.5       rlang_0.4.12        jquerylib_0.1.4    
#> [10] bslib_0.3.1         rmarkdown_2.11      tools_4.1.1        
#> [13] stringr_1.4.0       xfun_0.27           yaml_2.2.1         
#> [16] fastmap_1.1.0       compiler_4.1.1      BiocManager_1.30.16
#> [19] htmltools_0.5.2     knitr_1.36          sass_0.4.0