Changelog

Source: NEWS.md

RmzTabM version 0.99

Changes in version 0.99.3

• Add function mzTabMValidator() for the validation of the MzTab-M files before the import and after the export.

Changes in version 0.99.2

• Adding support to "mzTab-profile" field.

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
• Fix issue #46
• Fix issue #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.