# RmzTabM version 0.99

## Changes in version 0.99.1

- Address Bioconductor review process comments.

## Changes in version 0.99.0

- Bioconductor submission.

# RmzTabM version 0.97

## Changes in version 0.97.20

- Preparation to Biocondutor submission.

## Changes in version 0.97.19

- Fix issue [#45](https://github.com/rformassspectrometry/RmzTabM/issues/45)
- Fix issue [#46](https://github.com/rformassspectrometry/RmzTabM/issues/46)
- Fix issue [#47](https://github.com/rformassspectrometry/RmzTabM/issues/47)
- Add method to handle sml/sme in MzTabM object.

## Changes in version 0.97.18

- Initial version of `makeSummarizedExperimentFromMzTabM()` to convert `mzTabM`
  object with MTD+SMF to `SummarizedExperiment`.
- Add helper function `mtdToSampleData()`, inverse function of
  `mtdFromSampleData()`.
- Fix minor bug `mtdFromSampleData`.
- Update tests and vignette.

## Changes in version 0.97.17

- Update and simplify the `SummarizedExperiment` export example in the vignette.

## Changes in version 0.97.16

- Update vignette with high-level functionality to export a mzTab-M file.
- Add helper functions `.NAtonull()`.
- Add `as.list()`.
- Fix bug in instrument field sorting.
- Support `identifier` for optional columns in SML, SMF, SME.
- Update `readMzTabM()` to create a `MzTabM` object.
- Update tests and examples.

## Changes in version 0.97.15

- Add functionality to generate mzTab-M content from a `SummarizedExperiment`.

## Changes in version 0.97.14

- Refactor `setMtdInstrument()`, `setMtdDatabase()`, `setMtdCv()`,
  `setMtdContact()`, `setMtdField()` as method.

## Changes in version 0.97.13

- Add function `mtdFromSampleData()` to create metadata (MTD) content including
  sample, MS run, assay and study variable information from a *sample data*
  `data.frame`.

## Changes in version 0.97.12

- Add fucntion `mtdProtocol()` for MTD section.
- Update regex for CV parameter.
- Support `ms_run-parameter`, `assay-protocol_ref`, `assay-parameter`,
  `study_variable-ms_run_ref` and `contact-orcid`.
- Update tests and examples.

## Changes in version 0.97.11

- Add `MzTabM` class as a container for mzTab-M content.

## Changes in version 0.97.10

- First version of general read function `readMzTabM()`
- Add example and tests.
- Fix bug related `study_variable[1-n]-group_ref`
- Change type `study_variable_group[1-n]` to CV param

## Changes in version 0.97.9

- Support `"Parameter"` as study variable group datatype.
- Automatic datatype definition for study variable group supports `"Parameter"`.

## Changes in version 0.97.8

- Add functions `setMtdInstrument()`, `setMtdDatabase()`, `setMtdCv()`, `setMtdContact()`,
  `setMtdField()` and `updateMtdContent()` for MTD section
- Add examples and tests.

## Changes in version 0.97.7

- Add SME section code.
- Add scripts to test export of mzTab-M 2.1 files.

## Changes in version 0.97.6

- MTD: add *study_variable_group* support (mzTab-M >= 2.1).
- MTD: add STATO as one of the default CV ontologies.

## Changes in version 0.97.5

- Add functionality to create/format the SML section: `sml_create()`,
  `sml_sort()`, `sml_add_study_variable_columns()`.

## Changes in version 0.97.4

- Restructure helper functions to be usable across SMF and SML functionality.

## Changes in version 0.97.3

- Add utility function `parse_cv_param()`.

## Changes in version 0.97.2

- Add vignette.

## Changes in version 0.97.1

- Addition of SMF related functions to the package.

## Changes in version 0.97.0

- Move code for metadata creation and formatting from the *lifs-tools/rmzTabM*
  repository.
