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