Version 1.15.2
----------------------------
o Bug fixes for duplicate column names
Version 1.15.1
----------------------------
o New m/z shift modeling functionality added:
+ mzFit(): m/z shift modeling and plotting function
+ mzfitParam(): parameter list function for listing modeling parameters
o update to calcScores():
+ new arguments (mzshift and mzfit) for m/z correction before scoring
o new citation
Version 1.11.1
----------------------------
o m/z group size limit eliminated (previous: 10000 maximum)
Version 1.9.2
----------------------------
o featdata slot renamed to featData
o associated methods also renamed:
+ adductdata() -> adductData()
+ iddata() -> idData()
+ featdata() -> featData()
+ mzdata() -> mzData()
+ Qdata() -> QData()
+ rtdata() -> rtData()
o new method combineData():
+ merges columns from combinedTable() and featData()
Version 1.9.1
----------------------------
o 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
o new function opts.duplicate():
+ lists default parameters for duplicate feature handling in metabData()
+ new duplicate feature merging option (opts.duplicate(resolve = "merge"))
o Minor Change to evaluateParams():
+ "score" column changed to "totalScore" (for clarity)
Version 1.7.1
----------------------------
o Addition of filtered features to metabData objects and filtered method
o Bug Fix in metabData():
+ zero values now treated as missing in Q calculations (zero = TRUE)
o Bug Fix in calcScores()/ evaluateParams():
+ rtrange calculations now account for missing values
o Bug Fix in reduceTable()/ reduceTableParam():
+ method argument included with "mzrt" option
o small logic fix in labelRows() / reduceTable()
+ previous version caused duplicate feature matches in rare cases
Version 1.5.2
-----------------------
o Bug Fix in fit_model():
+ rtx & rty parameter issue resolved
Version 1.5.1
-----------------------
o New function updateTables():
+ user changes to combinedTable report
+ inclusion of non-intersected features
o Changes in metabCombiner():
+ handling of missing features enabled (i.e. when update() is used)
+ new argument "impute"
+ rtOrder argument bug fix
o Changes in metabCombine():
+ new arguments "union" & "impute"
o Changes in fit_model/ fit_gam()/ fit_loess():
+ new arguments rtx & rty
o Changes in batchCombine():
+ new argument "union"
+ expected multiple (2 or more) datasets as input
+ end message added
o Changes in labelRows()/ reduceTable()/ labelRowParam()/ reduceTableParam():
+ new argument 'useID'
+ 'resolveConflicts' and 'remove' set to TRUE in reduceTable()
o Changes to metabData objects:
+ "extra"" column count added to show() message
o Package functions updated to handle "group 0"
Version 1.3.2
---------------------
o Changes to labelRows():
+ new resolveConflicts + rtOrder arguments
+ column names duplication of {labels, subgroup, alt} eliminated
o Changes to metabCombiner()/ metabCombine():
+ resolveConflicts method applied to metabCombiner object
+ new rtOrder argument
Version 1.3.1
----------------------
o Changes to fit_gam()/ fit_loess():
+ message() used in place of cat()
o Changes to metabCombiner() & combinedTable / featdata slots:
+ new rowID column added
o Changes to calcScores() / evaluateParams() / labelRows()/ reduceTable():
+ new rowID checks
o Changes to write2file():
+ combinedTable & featdata merged by rowID column (metabCombiner inputs)
Version 1.1.4 (2021-5-18)
-------------------------------
o Multi-dataset support and batchCombine added to metabCombiner package.
o Changes to metabCombiner-class:
+ new slots "featdata", "datasets", "xy"
o New metabCombiner object methods:
+ datasets, x, y, featdata, iddata, mzdata, rtdata, Qdata, adductdata
o New reduceTable()/ reduceTableParam() function
o New batchCombine() function
o Changes to object methods (getExtra, getSamples, nonmatched):
+ default data argument value changed to NULL
+ if data = NULL, returns full list pertaining to object slot
o Changes to data.R:
+ new object "metabBatches"
o Changes to metabCombiner():
+ xdata & ydata arguments accept metabCombiner objects as inputs
+ featdata constructed alongside combinedTable
+ new arguments: xid, yid, means
+ faster combinedTable construction
o Changes to labelRows()/ labelRowsParam():
+ new argument "maxRTerr""
o Changes to plot_fit():
+ bug fix for outlier highliting
+ new "legend" argument
o Changes to write2file():
+ merges combinedTable with featdata (metabCombiner object inputs)
+ faster data parsing with tidyr::unite
o CITATION added
o numerous changes to documentation, parameter & error checking
Version 1.1.3 (2021-1-13)
-------------------------------
o new metabCombine() wrapper function
o new parameter list functions for loading main function defaults
o Changes to labelRows():
+ "conflict" argument replaced with "delta", with default value (0.2)
+ default value of "minScore" argument increased to 0.5
o Changes to calcScores():
+ default argument values set: A (75), B (10), C (0.25)
o Changes to fit_loess():
+ new argument "control"
- "iterLoess" parameter removed
o Changes to selectAnchors():
+ default "tolrtq" value changed: 0.5 -> 0.3
Version 1.1.2 (2020-12-28)
-------------------------------
o Changes to fit_gam()/ fit_loess():
+ new "outlier" argument
+ altered argument names: "frac" -> "prop", "ratio" -> "coef"
+ documentation and minor code changes
o Changes to plot_fit():
+ new outlier argument
- remove.outliers argument removed
o new test case for fit_gam()
Version 1.1.1 (2020-12-02)
-------------------------------
o Bug Fixes:
+ combinedTable check for missing group values
+ calcScores / evaluateParams groups argument fix
+ warning for column names with bracket characters "{ ( [ ] ) }"
+ QCol bug in metabData
o New Functionality
+ getExtra method added to metabCombiner objects (Issue #11)
Version 1.0.0 (2020-10-20)
------------------------------
o Accepted to Bioconductor
o Changes to metabData():
+ matrixStats package used with notable improvements to metabData()
+ rtmin or rtmax out of bounds warning replaced with error
Changes in version 0.99.0 (2020-09-11)
------------------------------------------
+ Submitted to Bioconductor