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Merge pull request #13 from rformassspectrometry/alabaster
Add alabaster support to MsIO (issue #12)
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Package: MsIO | ||
Title: Serializing and restoring/importing mass spectrometry data objects | ||
Version: 0.0.2 | ||
Version: 0.0.4 | ||
Authors@R: | ||
c(person(given = "Johannes", family = "Rainer", | ||
email = "[email protected]", | ||
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@@ -15,20 +15,23 @@ Authors@R: | |
role = "ctb", | ||
comment = c(ORCID = "0000-0002-1520-2268"))) | ||
Description: The serialization mechanism of R allows to save and load R data | ||
objects in a binary format, that can however not read by other | ||
objects in a binary format, that can however not be read by other | ||
programming languages or software. The MsIO package supports | ||
serializing and restoring or importing mass spectrometry data | ||
objects to and from language agnostic file formats. The file type | ||
can be defined and configured through a second argument `param` | ||
of the export/import methods. | ||
objects to and from language agnostic file formats. A variety | ||
of different file types, including HDF5 and JSON-based formats | ||
defined by the Bioconductor *alabaster* package are supported. The | ||
file type can be defined and configured through a second argument | ||
`param` of the export/import methods. | ||
Depends: | ||
R (>= 4.2.0) | ||
Imports: | ||
jsonlite, | ||
methods, | ||
MsCoreUtils, | ||
MsCoreUtils (>= 1.17.1), | ||
S4Vectors, | ||
ProtGenerics, | ||
S4Vectors | ||
alabaster.base | ||
Suggests: | ||
BiocStyle (>= 2.5.19), | ||
faahKO, | ||
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@@ -37,9 +40,11 @@ Suggests: | |
msdata, | ||
rmarkdown, | ||
roxygen2, | ||
Spectra, | ||
Spectra (>= 1.15.6), | ||
testthat, | ||
xcms | ||
xcms, | ||
alabaster.se, | ||
alabaster.matrix | ||
License: Artistic-2.0 | ||
Encoding: UTF-8 | ||
VignetteBuilder: knitr | ||
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@@ -49,10 +54,13 @@ biocViews: Infrastructure, MassSpectrometry, Metabolomics, DataImport, Proteomic | |
Roxygen: list(markdown=TRUE) | ||
RoxygenNote: 7.3.2 | ||
Collate: | ||
'PlainTextParam.R' | ||
'AlabasterParam.R' | ||
'AllGenerics.R' | ||
'MsBackend.R' | ||
'PlainTextParam.R' | ||
'MsBackendMzR.R' | ||
'MsExperiment.R' | ||
'MsExperimentFiles.R' | ||
'Spectra.R' | ||
'XcmsExperiment.R' | ||
'zzz.R' |
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# Version 0.0 | ||
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## Changes in 0.0.4 | ||
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- Add *alabaster* `saveObject()` and `readObject()` methods as well as | ||
`saveMsObject()` and `readMsObject()` methods with `AlabasterParam` param for | ||
`MsBackendMzR`, `Spectra`, `MsExperiment` and `XcmsExperiment` objects. | ||
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## Changes in 0.0.3 | ||
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- Implement `saveMsObject()` and `readMsObject()` with `PlainTextParam` for | ||
`MsBackendMzR`, `Spectra`, `MsExperiment` and `XcmsExperiment`. | ||
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## Changes in 0.0.2 | ||
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- Refactor code for text-based import and export of MS data objects. |
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