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Rgoslin Repository for Bioconductor submission

License: MIT License

R 2.96% C++ 79.57% C 0.42% ANTLR 14.19% Makefile 0.89% CSS 1.86% Batchfile 0.10%

rgoslin's Issues

Total.OH & LCB.OH counts are off and differ

Hi,
I am parsing some sphingolipids and noticed that the LCB double bonds are off.
I expected to find a total of 2 hydroxylations and 2 hydroxylations in the LCB.
However, rgoslin also reports different values for Cer compared to other lipid classes, even though the fatty acid component remains the same.

Thank you and best wishes,

Mathias

library(rgoslin)

lipid_names <- c("SM (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)

# Total
parsed_names[c("Normalized.Name", "Total.C", "Total.DB", "Total.OH")]
#>       Normalized.Name Total.C Total.DB Total.OH
#> 1     SM 18:1;O2/16:0      34        1        1
#> 2    Cer 18:1;O2/16:0      34        1        2
#> 3 GalCer 18:1;O2/16:0      34        1        1
#> 4 GlcCer 18:1;O2/16:0      34        1        1
#> 5 LacCer 18:1;O2/16:0      34        1        1

# LCB 
parsed_names[c("Normalized.Name", "LCB.C",  "LCB.DB","LCB.OH", "LCB.Bond.Type")]
#>       Normalized.Name LCB.C LCB.DB LCB.OH LCB.Bond.Type
#> 1     SM 18:1;O2/16:0    18      1      1           LCB
#> 2    Cer 18:1;O2/16:0    18      1      2           LCB
#> 3 GalCer 18:1;O2/16:0    18      1      1           LCB
#> 4 GlcCer 18:1;O2/16:0    18      1      1           LCB
#> 5 LacCer 18:1;O2/16:0    18      1      1           LCB

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

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.0 (2023-04-21)
#>  os       macOS Ventura 13.4
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#>  date     2023-06-02
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#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
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#>  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)
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#> 
#> ──────────────────────────────────────────────────────────────────────────────

Some lipids are interpreted with hydroxylations

Hi,

I am trying to implement Goslin at Lipotype to provide the shorthand2020 nomenclature to our customers. I largely works out of the box for our nomenclature, which always also provides the hydroxylations for every lipid (See below). However, for some (and only some) lipids this is misinterpreted. As a workaround, I can simply remove all 0 hydroxylations (";0") from the lipid names, however you should probably look at these special cases.

Keep up the good work!
Mathias

library(rgoslin)
# Some lipids are interpreter with OHs 

# Correct
parseLipidName("PC O-16:1;0/16:0;0")[[1]]
#> [1] "PC O-16:1/16:0"
# with OH
parseLipidName("PC O-16:0;0/16:0;0")[[1]]
#> [1] "PC O-16:0;OH/16:0;OH"


# Correct
parseLipidName("CE 16:1;0")[[1]]
#> [1] "SE 27:1/16:1"
# with OH
parseLipidName("CE 16:0;0")[[1]]
#> [1] "SE 27:1/16:0;OH"
parseLipidName("CE 14:0;0")[[1]]
#> [1] "SE 27:1/14:0;OH"
parseLipidName("CE 17:0;0")[[1]]
#> [1] "SE 27:1/17:0;OH"

sessionInfo()
#> R version 4.1.3 (2022-03-10)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS Monterey 12.3.1
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRblas.0.dylib
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#> 
#> other attached packages:
#> [1] rgoslin_0.99.3
#> 
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#> [17] xfun_0.30       yaml_2.3.5      fastmap_1.1.0   compiler_4.1.3 
#> [21] htmltools_0.5.2 knitr_1.38

^{Created on 2022-04-08 by the reprex package (v2.0.1)}

Incorrect parsing of TG species names when one FA is known (e.g. TG 16:0_34:1)

Hi Dominik,
parsing of e.g. TG 16:0_34:1 returns DG 16:0_34:1 under Normalized.Name and Molecular.Species.Name, DG 48:1 as Species.Name and DG as lipid classes. TG 16:0_16:0_18:1 and TG 40:1 however are parsed correctly. Thank you!

Compilation fails with gcc version 13.2.0

Hi,

I noticed that the compilation of the C++ library fails when using gcc version 13.2.0. I receive the following error message:

src/parser/ParserClasses.cpp:226:34: error: ‘size’ was not declared in this scope
  226 |     return Bitfield::iter(*this, size());
      |                                  ^~~~
make[1]: *** [makefile:57: src/domain/LipidClasses.cpp] Error 1
make[1]: Leaving directory '/tmp/RtmpTIGAtS/R.INSTALL81392a2ba4/rgoslin/src/cppgoslin'
make: *** [Makevars:25: sublibraries] Error 1
ERROR: compilation failed for package ‘rgoslin’
* removing ‘/usr/local/lib/R/site-library/rgoslin’

When I downgrade gcc to version 11.4, it compiles fine.

New names after parsing

I am trying to analyze a lipidomics dataset using lipidr and after I create the lipidomics experiment object I get the following warning
"Some lipid names couldn't be parsed because they don't follow the pattern 'CLS xx:x/yy:y'
Cer 40:1;O2, Cer 42:2;O2, HexCer 40:1;O2, LPE O-16:1, LPE O-18:1, PC O-32:1, PC O-34:1, PC O-16:0_18:2, PC O-16:1_18:1, PC O-34:3, PC O-36:1, PC O-36:2, PC O-36:4, PC O-36:5, PC O-38:4, PC O-38:5, PE O-34:2, PE O-36:3, PE O-36:5, PE O-38:5, PE O-38:7, PE O-40:7, SM 32:1;O2, SM 32:2;O2, SM 33:1;O2, SM 34:0;O2, SM 34:1;O2, SM 34:2;O2, SM 35:1;O2, SM 36:1;O2, SM 36:2;O2, SM 36:3;O2, SM 38:1;O2, SM 39:1;O2, SM 40:1;O2, SM 16:1;O2/24:1, SM 18:2;O2/22:0, SM 41:1;O2, SM 41:2;O2, SM 42:1;O2, SM 42:2;O2, SM 42:3;O2, SM 43:1;O2".

After seeing a thread of yours in bioconductor I implement the following code:

old_names <- rowData(d)$Molecule
new_names <- rowData(d)$clean_name %>% str_match(pattern="([\\w :-]+)(\\(\\w+\\))?")
normalized_new_names <- new_names[,2] %>% parseLipidNames(.)

lpd <- update_molecule_names(d, old_names, normalized_new_names$Normalized.Name)

rowData(lpd)$Class <- normalized_new_names$Lipid.Maps.Main.Class
rowData(lpd)$Category <- normalized_new_names$Lipid.Maps.Category
rowData(lpd)$Molecule <- normalized_new_names$Normalized.Name
rowData(lpd)$LipidSpecies <- normalized_new_names$Species.Name
rowData(lpd)$Mass <- normalized_new_names$Mass
rowData(lpd)$SumFormula <- normalized_new_names$Sum.Formula

Lipids seem to be parsed but I am encountering the two following issues:

CE class is renamed to SE 27:1, e.g. CE 16:0 renamed to SE 27:1/16:0

2.Lipids with two or more FAs keep only the first FA, e.g. PC 16:0_18:3 to PC 16:0 and TG 16:0_18:2_22:5 to TG 16:0

Could you offer some guidance, please?

rgoslin can parse `GM1(d18:1/16:0)` but not its normalised name `GM1 18:1;O2/16:0`

Hi,

This could be in relation to #15

I am using the rgoslin version 1.0.1, install directly from github via devtools

It seems strange that while rgoslin is able to parse GM1 (and some GSL classes) in the form GM1(d18:1/16:0) giving the output normalised name as GM1 18:1;O2/16:0, it is unable to parse GM1 in the form of its normalised name GM1 18:1;O2/16:0.

The same applies for GM3

library(rgoslin)

parseLipidNames("GM1(d18:1/16:0)")[["Normalized.Name"]]
#> [1] "GM1 18:1;O2/16:0"

parseLipidNames("GM1 18:1;O2/16:0")[["Normalized.Name"]]
#> Encountered an error while parsing 'GM1 18:1;O2/16:0': Expecting a single string value: [type=character; extent=4].
#> [1] NA

parseLipidNames("GM3(d18:1/16:0)")[["Normalized.Name"]]
#> [1] "GM3 18:1;O2/16:0"

parseLipidNames("GM3 18:1;O2/16:0")[["Normalized.Name"]]
#> Encountered an error while parsing 'GM3 18:1;O2/16:0': Expecting a single string value: [type=character; extent=4].
#> [1] NA

sessionInfo()
#> R version 4.2.1 (2022-06-23 ucrt)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 10 x64 (build 19044)
#> 
#> Matrix products: default
#> 
#> locale:
#> [1] LC_COLLATE=English_Singapore.utf8  LC_CTYPE=English_Singapore.utf8   
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#> [5] LC_TIME=English_Singapore.utf8    
#> 
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^{Created on 2022-07-27 by the reprex package (v2.0.1)}

Some GSL Classes do not work

Hi Rgoslin Team,

some of the GSL classes below do not work for me.
They are listed in the supplement table of your publication:

Kopczynski, Dominik, Nils Hoffmann, Bing Peng, Gerhard Liebisch, Friedrich Spener, and Robert Ahrends. “Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures.” Analytical Chemistry, April 11, 2022. https://doi.org/10.1021/acs.analchem.1c05430.

They should work, right?

Thank you and cheers,

Mathias

library(rgoslin)

# Working
parseLipidNames("SM 36:1;2")[[1]]
#> [1] "SM 36:1;O2"
parseLipidNames("GM3 36:1;2")[[1]]
#> [1] "GM3 36:1;O2"

# Working
parseLipidNames("GD3 36:1;2")[[1]]
#> [1] "GD3 36:1;O2"
# Not working
parseLipidNames("GD1 36:1;2")[[1]]
#> Encountered an error while parsing 'GD1 36:1;2': Expecting a single string value: [type=character; extent=4].
#> [1] NA
parseLipidNames("GD2 36:1;2")[[1]]
#> Encountered an error while parsing 'GD2 36:1;2': Expecting a single string value: [type=character; extent=4].
#> [1] NA

# Working
parseLipidNames("GM3 36:1;2")[[1]]
#> [1] "GM3 36:1;O2"
parseLipidNames("GM1 36:1;2")[[1]]
#> [1] "GM1 36:1;O2"
# Not working
parseLipidNames("GM2 36:1;2")[[1]]
#> Encountered an error while parsing 'GM2 36:1;2': Expecting a single string value: [type=character; extent=4].
#> [1] NA

# Not working
parseLipidNames("GT1 36:1;2")[[1]]
#> Encountered an error while parsing 'GT1 36:1;2': Expecting a single string value: [type=character; extent=4].
#> [1] NA
parseLipidNames("GT2 36:1;2")[[1]]
#> Encountered an error while parsing 'GT2 36:1;2': Expecting a single string value: [type=character; extent=4].
#> [1] NA
parseLipidNames("GT2 36:1;2")[[1]]
#> Encountered an error while parsing 'GT2 36:1;2': Expecting a single string value: [type=character; extent=4].
#> [1] NA

^{Created on 2022-05-18 by the reprex package (v2.0.1)}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.1.3 (2022-03-10)
#>  os       macOS Monterey 12.4
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#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
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#>  date     2022-05-18
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#> ──────────────────────────────────────────────────────────────────────────────

LIPID MAPS Main Class for Deoxyceramide/Cer m/Cer XX:X;O is unexpectedly in Other Sphingolipids [SP00] instead of Ceramides [SP02]

Referencing issue from previous repository:

lifs-tools/rgoslin-old#11

Possible parsing error for TAGs with one specified fatty acid

Hi,

When using Rgoslin v1.6.0 for parsing triacylglycerols where only one fatty acid is explicitly given (e.g. TG 20:1_52:1), the lipid class is recognized as diacylglycerol.

E.g. the following command will lead to the parsed results below:
parseLipidNames("TG 20:1_52:1")

Normalized.Name: DG 20:1_52:1
Original.Name : TG 20:1_52:1
Lipid.Maps.Category : GL
Lipid.Maps.Main.Class: DG
Species.Name : DG 72:2
Molecular.Species.Name: DG 20:1_52:1
Total C: 72
Total DB: 2
Mass: 1125.101
Sum Formula: C75H144O5
FA1.C: 20
FA1.DB: 1
FA2.C: 52
FA2.DB: 1

This behaviour is consistent across all TAGs that I have tested (ca. 500). isValidLipidName() is not complaining about the nomenclature, and in previous versions, the parsing has worked.
Is this a new shorthand nomenclature or maybe a bug?

Adding `LHex2Cer` and `LHex3Cer` to the grammar

Hi Dominik,
just realised LHex2Cer and LHex3Cer (which includes e.g. lyso-Gb3) are not in dictionary. Possible to add these species too?

ACers do not work on species level

Hi gosling Team,

I have one more: I get an error, when trying to provide a Acylceramide string.

Thank you for your help!

library(rgoslin)


# Working
parseLipidNames("Cer 36:1;2")[[1]]
#> [1] "Cer 36:1;O2"
parseLipidNames("Cer 67:2;2")[[1]]
#> [1] "Cer 67:2;O2"
# Not working
parseLipidNames("ACer 67:2;2")[[1]]
#> Encountered an error while parsing 'ACer 67:2;2': Expecting a single string value: [type=character; extent=4].
#> [1] NA

^{Created on 2022-05-25 by the reprex package (v2.0.1)}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.1.3 (2022-03-10)
#>  os       macOS Monterey 12.4
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
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#>  date     2022-05-25
#>  pandoc   2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
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#>  cli           3.3.0   2022-04-25 [2] CRAN (R 4.1.1)
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#>  rgoslin     * 1.0.1   2022-05-20 [1] Github (lifs-tools/rgoslin@b449c41)
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LHexCer 18:1;O2 is not parseable

Hi,

when I run the lines below, then 1 and 2 are fine, but 3 returns NOT_PARSEABLE, even for 1 and 2 LHexCer 18:1;O2 is returned in Normalized.Name. Is this an expected behaviour? Thank you for your time!

1) parseLipidNames("LHexCer d18:1")
2) parseLipidNames("LHexCer 18:1;2")
3) parseLipidNames("LHexCer 18:1;O2")

data.frame vs tibble

Hi,

one thing I found by using rgoslin is that parseLipidName() returns a data.frame, while parseLipidNames() returns a tibble. I would suggest to replace dplyr::bind_rows(namesList) with do.call(rbind, list(namesList)) which returns a data.frame

Here an example for illustration:

lipidNames <- list(parseLipidName("PC 16:0_16:1"),
                   parseLipidName("PC 16:0_16:2"),
                   parseLipidName("PC 16:1_16:1"))

do.call(rbind, lipidNames)

Gb3 class is reported as "Cer".

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

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)
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#>  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)
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#>  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
#> 
#> ──────────────────────────────────────────────────────────────────────────────

lifs-tools / rgoslin Goto Github PK

rgoslin's Issues

Total.OH & LCB.OH counts are off and differ

Some lipids are interpreted with hydroxylations

Incorrect parsing of TG species names when one FA is known (e.g. TG 16:0_34:1)

Compilation fails with gcc version 13.2.0

New names after parsing

rgoslin can parse `GM1(d18:1/16:0)` but not its normalised name `GM1 18:1;O2/16:0`

Some GSL Classes do not work

LIPID MAPS Main Class for Deoxyceramide/Cer m/Cer XX:X;O is unexpectedly in Other Sphingolipids [SP00] instead of Ceramides [SP02]

Possible parsing error for TAGs with one specified fatty acid

Adding `LHex2Cer` and `LHex3Cer` to the grammar

ACers do not work on species level

Dependency Dashboard

Open

LHexCer 18:1;O2 is not parseable

data.frame vs tibble

Gb3 class is reported as "Cer".

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