Updates: Version 1.3.2 --------------------- Changes to labelRows(): + new resolveConflicts + rtOrder argument added for automated resolution of conflicting feature pair alignment fows in combinedTable, with embedded C function (resolveRows.c) + new argument rtOrder paired with resolveConflicts determines if RT order consistency is expected when resolving alignment conflicts + duplicate column names for {labels, subgroup, alt} removed and no longer allowed in resulting combinedTable Changes to metabCombiner(): + new check for metabCombiner object inputs: labelRows must be called before aligning a metabCombiner object with a new dataset + resolveConflicts method applied to metabCombiner object to eliminate conflicting alignments/ attain 1-1 matches for all features + new rtOrder argument controlling resolveConflicts similar to above Version 1.3.1 ---------------------- Changes to fit_gam()/ fit_loess(): + messages changed from using cat() to using message() Changes to metabCombiner() & combinedTable / featdata slots: + rowID column now the first column in both tables instead of having this information be the row names Changes to calcScores() / evaluateParams() / labelRows(): + updated to reflect above changes to keep rowID identical between combinedTable & featdata Changes to write2file(): + combinedTable & featdata merged by rowID column when metabCombiner objects used as input Version 1.1.4 (2021-5-18) ------------------------------- Multi-dataset support and batchCombine added to metabCombiner package. Changes to metabCombiner-class: + new slot "featdata" for feature descriptor (id,mz,rt,Q,adduct) tracking + new slot "datasets" for dataset ID tracking + new slot "xy" for tracking current x & y dataset labels New metabCombiner methods: + datasets: retrieves dataset identifiers from metabCombiner object + x: retrieves identifier of current x dataset + y: retrieves identifier of current y dataset + featdata: retrieves all feature meta-data or from one dataset + iddata: retrieves all feature identities or identities from one dataset + mzdata: retrieves all feature m/z values or m/z values from one dataset + rtdata: retrieves all feature rt values or rt values from one dataset + Qdata: retrieves all feature Q values or Q values from one dataset + adductdata: retrieves all adduct labels or adduct labels from one dataset New reduceTable()/ reduceTableParam() functions: + variant of labelRows where reduce argument automatically set to TRUE + defaults are the same as labelRows()/ labelRowsParam(), except for rank thresholds (set to 2 for maxRankX & maxRankY) New batchCombine() function: + method for automated sequential alignment of metabolomics batch datasets + modeled after metabCombine function, but takes a list of metabData objects as input and applies reduceTable with reduceTableParam() parameter inputs 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" - a list of three batch data frame for use as an example dataset for batchCombine() Changes to metabCombiner(): + xdata & ydata arguments now accept metabCombiner objects as inputs + featdata slot constructed alongside combinedTable at this step + xid & yid arguments added for individual dataset naming (metabData) or specifying active x & y dataset to use for analysis (metabCombiner) + option to average m/z, rt, & Q for metabCombiner object inputs + faster metabCombiner table construction Changes to labelRows()/ labelRowsParam(): + new argument maxRTerr for annotating/ removing feature pair alignment rows with excessive retention time fitting errors Changes to plot_fit(): + bug fix for highlighting outliers + new legend argument for specifying points on the legend Changes to write2file(): + when metabCombiner objects provided as input, merges the combinedTable with featdata in output file for printing + faster data pasting with tidyr::unite CITATION added numerous other changes to documentation, parameter & error checking Version 1.1.3 (2021-1-13) ------------------------------- Package additions: + metabCombine(): main package workflow wrapper function + Parameter list functions for loading defaults of main workflow methods 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 for A (75), B (10), C (0.25) Changes to fit_loess(): + new argument "control" for controlling loess fit (list argument) - eliminated "iterLoess" parameter Changes to selectAnchors(): + default for "tolrtq" argument changed from 0.5 to 0.3 Version 1.1.2 (2020-12-28) ------------------------------- Changes to fit_gam()/ fit_loess(): + new outlier detection method based on boxplot / IQR added + new argument: outlier, which accepts "MAD" or "boxplot" as a value + altered argument names: "frac" to "prop", "ratio" to "coef" + documentation and minor code changes to main and supporting functions Changes to plot_fit(): + new options for showing, hiding, or highlighting (with a legend) outliers + new arguments: outlier, which accepts "show" / "s", "remove" / "r", or "highlight" / "h" as arguments ; ocol, outlier point color if outlier argument set to "highlight" / "h" - remove.outliers argument removed Other changes: + new test case for fit_gam() Version 1.1.1 (2020-12-02) ------------------------------- Bug Fixes: + combinedTable check for missing group values (Issue #7) + calcScores / evaluateParams groups bug (Issue #8) + Warning for column names with bracket characters "{ ( [ ] ) }" (Issue #9) + QCol bug (Issue #10) New Functionality + getExtra method added to metabCombiner objects (Issue #11) Version 1.0.0 (2020-10-20) ------------------------------ +Accepted to Bioconductor Functionality changes: + matrixStats function implementations for matrix calculations replace base implementations where appropriate, with notable improvements in adjustData() function within metabData() + filterRT() now gives an error rather than a warning if rtmin or rtmax are out of the bounds of the dataset RTs Changes in version 0.99.0 (2020-09-11) ------------------------------------------ + Submitted to Bioconductor