In this version, we just added a new function output_eic(). This can be used to generate peaks in some samples after you run process_data(). For example, you analyzed data, and found some features are very important, so you want to check the peak shapes of them in QC samples, so you can use output_eic() function.

Set work directory

First, you need to set the work directory to the folder which you used to run the process_data() function. For example, in our example for process_Data, we set the work directory in example/POS, so here, we also set work directory in this folder.

Run output_eic()

Then we can run output_eic() function.


output_eic(path = ".", 
           query_sample_name = c("QC_1"), 
           query_peak_name = c("M70T54_POS", "M70T579_POS"),
           polarity = "positive", 
           threads = 4)

Then the peak shape of plots will be outputted in example/POS/Result.

Session information

#> R Under development (unstable) (2022-01-11 r81473)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur/Monterey 10.16
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] rprojroot_2.0.2   digest_0.6.29     crayon_1.4.2      R6_2.5.1         
#>  [5] jsonlite_1.7.2    magrittr_2.0.1    evaluate_0.14     stringi_1.7.6    
#>  [9] rlang_0.4.12      cachem_1.0.6      fs_1.5.2          jquerylib_0.1.4  
#> [13] bslib_0.3.1       ragg_1.2.1        rmarkdown_2.11    pkgdown_2.0.1    
#> [17] textshaping_0.3.6 desc_1.4.0        tools_4.2.0       stringr_1.4.0    
#> [21] purrr_0.3.4       yaml_2.2.1        xfun_0.29         fastmap_1.1.0    
#> [25] compiler_4.2.0    systemfonts_1.0.3 memoise_2.0.1     htmltools_0.5.2  
#> [29] knitr_1.37        sass_0.4.0