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View Code? Open in Web Editor NEWThe R-language bindings for mzTab-M
Home Page: https://lifs-tools.github.io/rmzTab-m/
License: MIT License
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Metadata parsing: database name not parsed
Hi,
in an mzTab exported by [MS, MS:1003082, MS-DIAL, 3.98] the metabolite databases
are listed. In the metadata object metadata$database[[1]] the name "User-defined MSP library file" is missing.
Not sure if that is an issue with the generated mzTab or the reading by rmzTab.
Yours,
Steffen
| MTD | database[1] | [,, User-defined MSP library file, ] |
|---|---|---|
| MTD | database[1]-prefix | MSP |
| MTD | database[1]-version | Unknown |
| MTD | database[1]-uri | file://C:/MoNA.msp |
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Dependency: openapi
Hi, docs and DESCRIPTION need information about library(openapi):
Line 65 in 30d5208
I couldn't locate that package :-(
Yours, Steffen
undefined columns selected when fromDataFrame() without SME section
For a file exported by MS-Dial 3.98 from TripleQ data without SME section I get for
mzTabTable <- readMzTab(mzTabfile)
## To turn these tables into objects, use the R6 class constructor method `new()`:
mzTabObject <- MzTab$new()$fromDataFrame(mzTabTable)
The traceback
7: stop("undefined columns selected")
6: `[.data.frame`(df, , colnames(df) != "") at read_mz_tab.R#159
5: df[, colnames(df) != ""] at read_mz_tab.R#159
4: extractTable(mztab.table, "SEH", "SME") at read_mz_tab.R#187
3: extractSmallMoleculeEvidence(MzTabDataFrame) at mz_tab.R#210
2: MzTab$new()$fromDataFrame(mzTabTable) at #6
So
Line 159 in 660ca47
should check that there is an actual
df to speak of :-) PR coming.Yours, Steffen
Add examples to show how to create mzTab-M from XCMS and MSnbase objects
SMILES containing # quits parsing the remaining line
Hi, reading an mzTab in
Line 10 in d9cfc1e
fails if a SMILES contains an
# (as,e.g., in C#N, hydrogen cyanide, HCN)is interpreted as comment and skips the remaining line. PR coming up.
Yours, Steffen
convertMzTab2MAF() only handles mzTab with nrow(smlTable) == nrow(smfTable)
The function convertMzTab2MAF() is exporting the Abundances which are extracted
from the smlTable, while m/z and retention time come from the feature table.
The first version was assuming sml and smf had the same nrow() and ordering to avoid using any logic to put things together.
=> Tables should be linked via their IDs, and if multiple features are combined into one molecule, the average (or median ?) retention time should be calculated. PR coming.
Yours, Steffen.
Failure in assay
Hi, currently R CMD check fails in the test_assay.R with an
Fix error in tests 'safe_unbox' is not an exported object from 'namespace:rmzTabM'
but adding @export in https://github.com/lifs-tools/rmzTab-m/blob/development/R/json_utils.R#L3
gives a new error which could mean my quick fix was the wrong strategy:
2. Error: reading and writing of mztab json works (@test-
Only atomic vectors of length 1 or data frames with 1 row can be unboxed.
Backtrace:
1. rmzTabM::writeMzTabJSONToFile(mzTabObject, tmpfile)
4. mztab$toJSON()
5. self$metadata$toJSON()
6. base::lapply(self$assay, function(x) x$toJSON())
7. rmzTabM:::FUN(X[[i]], ...)
8. x$toJSON()
9. rmzTabM::safe_unbox(self$ms_run_ref)
── 3. Error: assay (@test_assay.R#27) ─────────────────────
$ operator is invalid for atomic vectors
Backtrace:
1. model.instance$toJSONString()
4. jsonlite::toJSON(...)
5. base::force(x)
General questions
Hi @nilshoffmann , just have some general questions a I would like to pick up import/export to/from mzTab-M in xcms...
-
would there be a possibility to avoid R6 classes in this package or to have general import/export/data handling functions supporting base R data types to allow an easier integration with other packages?
-
where could one best start to understand how to export data properly in mzTab format? Is there a nice use/case or uni test or example I could look at?
dplyr not imported
Hi, the code below works in the vignette because library(dplyr) is called manually.
## To turn these tables into objects, use the R6 class constructor method `new()`:
> mzTabObject <- MzTab$new()$fromDataFrame(mzTabTable)
Error in SummaryDataFrame %>% dplyr::select(dplyr::starts_with("abundance_assay")) :
could not find function "%>%"
Please expect PR soon.
Yours, Steffen
Adapt template for swagger-codegen to properly escape underscore names
mzTab-M without identification data?
Hi @nilshoffmann @sneumann - we're having some difficult time to export valid mzTab-M files from xcms. Basically, we're not having any identification data and thus the small molecule summary (SML) part is empty. We tried to create an SML table with a single entry and null values, but that does no pass the validator. Thus our questions:
- how should a mzTab-M file with only LC-MS feature abundances look like?
- (related) what is the best obo term to use for small_molecule-quantification_unit? In
xcmswe have arbitrary (semi-quantitative) abundances - and setting this to null does not work.
Any insights here would be great - especially because the validator throws an error, but we don't quite understand how to solve the issue.
Pinging also @philouail
Implement read from TSV support.
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