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