Gb3 class is reported as "Cer".

[dernesa]

Hi, also Gb3 class is reported as "Cer".

Thank you and best wishes,

Mathias

library(rgoslin)

lipid_names <- c("SM (d18:1/16:0)","Gb3 (d18:1/16:0)", "Cer (d18:1/16:0)", 
                 "GalCer (d18:1/16:0)", "GlcCer (d18:1/16:0)", "LacCer (d18:1/16:0)")

parsed_names <- parseLipidNames(lipid_names)

# classes
parsed_names[c("Normalized.Name", "Lipid.Maps.Main.Class")]
#>           Normalized.Name Lipid.Maps.Main.Class
#> 1         SM 18:1;O2/16:0                    SM
#> 2 Gal2GlcCer 18:1;O2/16:0                   Cer
#> 3        Cer 18:1;O2/16:0                   Cer
#> 4     GalCer 18:1;O2/16:0                GalCer
#> 5     GlcCer 18:1;O2/16:0                GlcCer
#> 6     LacCer 18:1;O2/16:0                LacCer

^{Created on 2023-06-02 with reprex v2.0.2}

Session info

``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.3.0 (2023-04-21) #> os macOS Ventura 13.4 #> system aarch64, darwin20 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Europe/Berlin #> date 2023-06-02 #> pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0) #> digest 0.6.31 2022-12-11 [1] CRAN (R 4.3.0) #> dplyr 1.1.2 2023-04-20 [1] CRAN (R 4.3.0) #> evaluate 0.21 2023-05-05 [1] CRAN (R 4.3.0) #> fansi 1.0.4 2023-01-22 [1] CRAN (R 4.3.0) #> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0) #> fs 1.6.2 2023-04-25 [1] CRAN (R 4.3.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0) #> htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.3.0) #> knitr 1.43 2023-05-25 [1] CRAN (R 4.3.0) #> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0) #> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) #> Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.3.0) #> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.3.0) #> rgoslin * 1.4.0 2023-04-25 [1] Bioconductor #> rlang 1.1.1 2023-04-28 [1] CRAN (R 4.3.0) #> rmarkdown 2.21 2023-03-26 [1] CRAN (R 4.3.0) #> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.3.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0) #> tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0) #> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0) #> utf8 1.2.3 2023-01-31 [1] CRAN (R 4.3.0) #> vctrs 0.6.2 2023-04-19 [1] CRAN (R 4.3.0) #> withr 2.5.0 2022-03-03 [1] CRAN (R 4.3.0) #> xfun 0.39 2023-04-20 [1] CRAN (R 4.3.0) #> yaml 2.3.7 2023-01-23 [1] CRAN (R 4.3.0) #> #> [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library #> #> ────────────────────────────────────────────────────────────────────────────── ```

[dominik-kopczynski]

Hi Mathias,

Thank you very much for spotting and reporting the issue. Yuup, this should not happen, however, I know why it does. I will fix it.

Cheers, Dominik

[dernesa]

Thank you!

[dominik-kopczynski]

Should be fixed now too in the development branch. With the next release, the fix will be in the main branch. Thank you very much again Mathias for your support :-)

[dernesa]

I checked it and it did work! ✓ Thank you!