NEWS.md

In sgibb/topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics

topdownr 1.25

Changes in version 1.25.1

• New version for Bioc 3.19 (devel)
• Adapt to fragment functions that are moved from MSnbase to PSMatch.

Changes in version 1.19.2

topdownr 1.19

Changes in version 1.19.2

• Avoid coercion methods that will be deprecated in Matrix 1.4-2.
• Replace stopifnot calls with if (...) stop calls.

Changes in version 1.19.1

• New version for Bioc 3.17 (devel)
• Rerun latest roxygen2.
• Remove if (getGeneric(...)) statements in AllGenerics.R do avoid problems while reloading the package.

topdownr 1.18

• New version for Bioc 3.14 (release)

topdownr 1.17

Changes in version 1.17.3

• Depending on mzR 2.27.5.
• Fix unit test for .readSpectrum to adapt to new mzR 2.27.5.

Changes in version 1.17.2

• Fix roxygen2 warnings.

Changes in version 1.17.1

• New version for Bioc 3.15 (devel)
• Adapt to new DFrame.

topdownr 1.16

• New version for Bioc 3.14 (release)

topdownr 1.15

Changes in version 1.15.1

• Add rmarkdown to Suggests:; see https://github.com/yihui/knitr/issues/1864 for details [2021-07-27].

topdownr 1.13

• New version for Bioc 3.13 (devel)

Changes in version 1.13.1

• as(..., "NCBSet") now treats neutral losses and modifications as bonds as well.
• readTopDownFiles gains a new argument customModifications to allow user-defined modifications. Suggestion and first implementation by Maša Babović [e-mail] [2021-03-15].

topdownr 1.12

• New version for Bioc 3.12 (release)

topdownr 1.11

• New version for Bioc 3.12 (devel)

topdownr 1.10

• New version for Bioc 3.11 (release)

topdownr 1.9

• New version for Bioc 3.11 (devel)

Changes in version 1.9.4

• Fix unit tests that check for "matrix" class. (class(m) now returns c("matrix", "array") in r-devel) [2019-12-17].

Changes in version 1.9.3

• Adapt analysis vignette to changed condition argument [2019-11-22].

Changes in version 1.9.2

• Set conditions="ScanDescription" as new default for readTopDownFiles. The creation of FilterString IDs in the method files was deprecated since over a year. conditions="FilterString" is still possible for backward-compatibility [2019-11-22].
• Fix error message handling in .validFilename and .translateThermoIdToScanId [2019-11-22].

Changes in version 1.9.1

• Remove defaultMs1Settings and defaultMs2Settings [2019-11-18].
• Fix .rbind for lists with mixed data.frame and DataFrame [2019-11-18].

topdownr 1.8

• New version for Bioc 3.10 (release)

topdownr 1.7

• New version for Bioc 3.10 (devel)

Changes in version 1.7.2

• Add readTopDownSet(..., conditions="ScanDescription") as a new way to read scan conditions (see #80/#81) [2019-08-08].

Changes in version 1.7.1

• Remove NEWS file (just keep NEWS.md).
• Never remove "AgcTarget" column from colData DataFrame.
• Strip white spaces from ScanHeadsman output.
• Defunct defaultMs1Settings and defaultMs2Settings. They will be removed in 3.11 [2019-06-19].

topdownr 1.6

• New version for Bioc 3.9 (release)

topdownr 1.5

• New version for Bioc 3.9 (devel)

Changes in version 1.5.6

• Revert changes for NULL indices of DataFrame introduced in 1.5.4 (a419f59, c4bfc1c) because they are fixed upstream in S4Vectors. Keep unit tests in place. [2019-03-27]

Changes in version 1.5.5

• Depends on R >= 3.5.0 now, because the seralization format changed in R.

Changes in version 1.5.4

• Fix for internal .makeRowNames/.colsToLogical/.colsToRle on DataFrame without any numeric/character columns.
• Fix unit test that uses set.seed (order changed during R-devel upgrade).

Changes in version 1.5.3

• biocViews: ImmunoOncology added by Kayla-Morrell [e-mail] [2019-01-04].

Changes in version 1.5.2

• Add expandMs1Conditions, expandTms2Conditions, createExperimentsFragmentOptimisation functions to allow more flexibility in method creation; see also #77 [2018-12-07].
• Modify interface/arguments of writeMethodXmls to adapt to new method creation workflow (the old interface will be defunct in Bioconductor 3.10 and removed in 3.11) [2018-12-07].
• Adapt the data-generation vignette to the new workflow [2018-12-07].
• Deprecated defaultMs1Settings and defaultMs2Settings. They will be defunct in Bioconductor 3.10 and removed in 3.11 [2018-12-07].

Changes in version 1.5.1

• readTopDownFiles gains the argument conditions to control wheter "FilterStrings" or a given number of conditions is used to create condition IDs; see #77 [2018-11-07].

topdownr 1.4

• New version for Bioc 3.8 (release)

topdownr 1.3

Changes in version 1.3.6

• Add Pavel's and Ole's ORCID to DESCRIPTION [2018-10-23].

Changes in version 1.3.5

• Fix format of roxygen links to foreign packages to avoid link warning in R CMD check [2018-10-10].

Changes in version 1.3.4

• Add inst/CITATION file [2018-09-26].

Changes in version 1.3.3

• Revert commit c6e8dfd: "Adapt to MSnbase 2.7.2 with internal fragments; see #82 [2018-06-03]."

Changes in version 1.3.2

• Use BiocManager::install [2018-07-16].

Changes in version 1.3.1

• Adapt to MSnbase 2.7.2 with internal fragments; see #82 [2018-06-03].
• Fix FragmentViews start/end/width and labels for internal fragments [2018-06-03].
• Fix as(tds, "MSnSet") unit test [2018-07-06].
• Use elementMetadata(..., use.names=FALSE) in combine,FragmentViews,FragmentViews-method to avoid duplicated rownames in elementMetadata slot [2018-07-06].

Changes in version 1.3.0

• New version for Bioc 3.8 (devel)

topdownr 1.2

Changes in version 1.2.0

• New version for Bioc 3.7 (release)

topdownr 1.1

Changes in version 1.1.7

• Add mz,FragmentViews-method [2018-02-01].
• Remove internal fragmentMass and fragmentNames functions [2018-02-22].
• Parse "spectrumId" column of the mzML header to find the scan number (instead of the "acquisitionNum") because ProteomDiscover generates non-standard "spectrumId" and proteowizard fails to translated it into a valid "acquisitionNum". See #73 for details [2018-02-22].
• Recalculate TotIonCurrent in the main loop of .readMzMl [2018-02-22].
• Add FragmentCoverage and BondCoverage columns to bestConditions,NCBSet-method [2018-02-23].
• Use retention times to test for correct matching between ScanHeadsman .txt output and mzML files; closes #74; [2018-02-23].

Changes in version 1.1.6

• Rotate fragment labels (vertical orientation) in plot [2018-01-17].
• Replace signature for updateMedianInjectionTime,TopDownSet-method to updateMedianInjectionTime,AbstractTopDownSet-method; closes #69; see also #71 [2018-01-27].
• Fix .matchFragments for length(fmass) == 0 [2018-01-27].
• Just plot fragments that are present in current TopDownSet see #70 [2018-01-27].
• Add combine,FragmentViews,FragmentViews-method [2018-01-27].
• Allow to combine TopDownSet objects with different fragment types; closes #71 [2018-01-27].
• Add all.equal for AbstractTopDownSet objects [2018-01-27].
• Allow the user to decide how to handle redundant fragment matching. Current default is redundantFragmentMatch="remove" and redundantIonMatch="remove". This will reduce the number of fragment matches. Choose "closest" for both to get the old behaviour. See also #72 [2018-01-29].
• TopDownSet object store the matching tolerance and strategies (redundantIonMatch, redundantFragmentMatch). AbstractTopDownSet and NCBSet lost their tolerance slot. Saved objects need to be recreated [2018-01-30].
• bestConditions,NCBSet-method returns a 5-column matrix now. Colums are: Index, FragmentsAddedToCombination, BondsAddedToCombination, FragmentsInCondition, BondsInCondition; see #52 [2018-01-30].

Changes in version 1.1.5

• Keep full filename (before basename was used) in AbstractTopDownSet objects [2017-12-28].
• Add plot,TopDownSet-method [2017-12-29].
• bestConditions,NCBSet-method gains a new argument maximise that allows to optimise for number of fragments or bonds covered (default: "fragments"); see #52 [2018-01-15].

Changes in version 1.1.4

• Add missing export of combine and documentation [2017-12-28].
• Resave tds example data set to reflect changes in colData introduced in version 1.1.2 [2017-12-28].

Changes in version 1.1.3

• Add conditionNames,AbstractTopDownSet-method to access rownames(colData(tds)) [2017-12-23].
• Add updateConditionNames,AbstractTopDownSet-method (closes #60) [2017-12-23].
• Turn updateMedianInjectionTime,TopDownSet-method into updateMedianInjectionTime,AbstractTopDownSet-method to work with TopDownSet and NCBSet objects [2017-12-27].
• Add combine,AbstractTopDownSet-method to combine multiple TopDownSet/NCBSet objects (closes #69) [2017-12-28].

Changes in version 1.1.2

• Add .rbind to combine scan and method information with different number of colums (could happen when CID/HCD and UVPD scans are taken independently with different software versions) [2017-12-22].
• Don't replace NA values with zeros in the colData [2017-12-22].
• Convert On/Off character columns in scan and method information to logical [2017-12-22].
• Fix .camelCase to avoid "TIC" to "TIc" and "UseCalibratedUVPDTimeMs2" to "UseCalibrateduvpdTimems2" conversion (now: "Tic" and "UseCalibratedUvpdTimeMs2") [2017-12-22].

Changes in version 1.1.1

• Respect assigned intensity in conditions for bestConditions,NCBSet-method and fragmentationMap (closes #62) [2017-12-02].
• Fix explanation of random forest barchart in analysis vignette [2017-12-02].
• Create all fragmentation methods in .readScanHeadsTable to avoid error if any is missing (fixes #68) [2017-12-20].
• Never remove Activation column in colData (even not if readTopDownFiles(..., dropNonInformativeColumns=TRUE)) [2017-12-20].
• Allow UVPD in fragmentationMap,NCBSet-method [2017-12-20].
• Add new method: updateMedianInjectionTime,TopDownSet-method (closes #66) [2017-12-20].

Changes in version 1.1.0

• New version for Bioc 3.7 (devel)

topdownr 1.0

Changes in version 1.0.0

• New version for Bioc 3.6 (release)

topdownr 0.9

Changes in version 0.99.0

• First public release.

sgibb/topdownr documentation built on Jan. 16, 2024, 12:14 a.m.