NEWS

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metabCombiner 1.15.2

• Bug fixes for duplicate column names

metabCombiner 1.15.1

• New m/z shift modeling functionality added: + mzFit(): m/z shift modeling and plotting function + mzfitParam(): parameter list function for listing modeling parameters
• update to calcScores(): + new arguments (mzshift and mzfit) for m/z correction before scoring
• new citation

metabCombiner 1.11.1

• m/z group size limit eliminated (previous: 10000 maximum)

metabCombiner 1.9.2

• featdata slot renamed to featData
• associated methods also renamed: + adductdata() -> adductData() + iddata() -> idData() + featdata() -> featData() + mzdata() -> mzData() + Qdata() -> QData() + rtdata() -> rtData()
• new method combineData(): + merges columns from combinedTable() and featData()

metabCombiner 1.9.1

• Changes to metabData(): + Major changes to duplicate feature handling + bug fix to existing duplicate filtering code + duplicate argument reworked to accept a list of parameters + option to merge duplicate feature rows added + duplicate features are filtered or merged before missingness filter + new rowID column added to metabData objects
• new function opts.duplicate(): + lists default parameters for duplicate feature handling in metabData() + new duplicate feature merging option (opts.duplicate(resolve = "merge"))
• Minor Change to evaluateParams(): + "score" column changed to "totalScore" (for clarity)

metabCombiner 1.7.1

• Addition of filtered features to metabData objects and filtered method
• Bug Fix in metabData(): + zero values now treated as missing in Q calculations (zero = TRUE)
• Bug Fix in calcScores()/ evaluateParams(): + rtrange calculations now account for missing values
• Bug Fix in reduceTable()/ reduceTableParam(): + method argument included with "mzrt" option
• small logic fix in labelRows() / reduceTable() + previous version caused duplicate feature matches in rare cases

metabCombiner 1.5.2

• Bug Fix in fit_model(): + rtx & rty parameter issue resolved

metabCombiner 1.5.1

• New function updateTables(): + user changes to combinedTable report + inclusion of non-intersected features
• Changes in metabCombiner(): + handling of missing features enabled (i.e. when update() is used) + new argument "impute" + rtOrder argument bug fix
• Changes in metabCombine(): + new arguments "union" & "impute"
• Changes in fit_model/ fit_gam()/ fit_loess(): + new arguments rtx & rty
• Changes in batchCombine(): + new argument "union" + expected multiple (2 or more) datasets as input + end message added
• Changes in labelRows()/ reduceTable()/ labelRowParam()/ reduceTableParam(): + new argument 'useID' + 'resolveConflicts' and 'remove' set to TRUE in reduceTable()
• Changes to metabData objects: + "extra"" column count added to show() message
• Package functions updated to handle "group 0"

metabCombiner 1.3.2

• Changes to labelRows(): + new resolveConflicts + rtOrder arguments + column names duplication of {labels, subgroup, alt} eliminated
• Changes to metabCombiner()/ metabCombine(): + resolveConflicts method applied to metabCombiner object + new rtOrder argument

metabCombiner 1.3.1

• Changes to fit_gam()/ fit_loess(): + message() used in place of cat()
• Changes to metabCombiner() & combinedTable / featdata slots: + new rowID column added
• Changes to calcScores() / evaluateParams() / labelRows()/ reduceTable(): + new rowID checks
• Changes to write2file(): + combinedTable & featdata merged by rowID column (metabCombiner inputs)

metabCombiner 1.1.4

• Multi-dataset support and batchCombine added to metabCombiner package.
• Changes to metabCombiner-class: + new slots "featdata", "datasets", "xy"
• New metabCombiner object methods: + datasets, x, y, featdata, iddata, mzdata, rtdata, Qdata, adductdata
• New reduceTable()/ reduceTableParam() function
• New batchCombine() function
• Changes to object methods (getExtra, getSamples, nonmatched): + default data argument value changed to NULL + if data = NULL, returns full list pertaining to object slot
• Changes to data.R: + new object "metabBatches"
• Changes to metabCombiner(): + xdata & ydata arguments accept metabCombiner objects as inputs + featdata constructed alongside combinedTable + new arguments: xid, yid, means + faster combinedTable construction
• Changes to labelRows()/ labelRowsParam(): + new argument "maxRTerr""
• Changes to plot_fit(): + bug fix for outlier highliting + new "legend" argument
• Changes to write2file(): + merges combinedTable with featdata (metabCombiner object inputs) + faster data parsing with tidyr::unite
• CITATION added
• numerous changes to documentation, parameter & error checking

metabCombiner 1.1.3

• new metabCombine() wrapper function
• new parameter list functions for loading main function defaults
• Changes to labelRows(): + "conflict" argument replaced with "delta", with default value (0.2) + default value of "minScore" argument increased to 0.5
• Changes to calcScores(): + default argument values set: A (75), B (10), C (0.25)
• Changes to fit_loess(): + new argument "control" - "iterLoess" parameter removed
• Changes to selectAnchors(): + default "tolrtq" value changed: 0.5 -> 0.3

metabCombiner 1.1.2 (2020-12-28)

• Changes to fit_gam()/ fit_loess(): + new "outlier" argument + altered argument names: "frac" -> "prop", "ratio" -> "coef" + documentation and minor code changes
• Changes to plot_fit(): + new outlier argument - remove.outliers argument removed
• new test case for fit_gam()

metabCombiner 1.1.1 (2020-12-02)

• Bug Fixes: + combinedTable check for missing group values + calcScores / evaluateParams groups argument fix + warning for column names with bracket characters "{ ( [ ] ) }" + QCol bug in metabData
• New Functionality + getExtra method added to metabCombiner objects (Issue #11)

metabCombiner 1.0.0 (2020-10-20)

• Accepted to Bioconductor
• Changes to metabData(): + matrixStats package used with notable improvements to metabData() + rtmin or rtmax out of bounds warning replaced with error

metabCombiner 0.99.0 (2020-09-11)

• Submitted to Bioconductor