Changelog • metaboMisc

metaboMisc 0.6.4

Added an export() method for the AnalysisData class.
Fixed a bug where file names were incorrectly converted from .raw to .mzML if “raw” was included in the file name alongside the extension.

suitableParallelPlan() is now re-exported from the jfmisc package. This now includes the RAM_per_worker and proportion_max_workers arguments to improve usability.

Fixed miss injection and batch correction detection for GC-MS data sets processed using xcms.
Fixed the feature summary for GC-MS data sets processed using xcms.

injOrder is now the default column for sample indexes returned from detectMissInjections().
The returned miss injection indexes are now sorted.
Fixed the MetaboProfile S4 class export() method for GC-MS techniques.
Added the strategy and workers arguments in suitableParallelPlan() to allow the manual selection of parallel options.
Added an export() method for the Construction S4 class.
detectModellingParameters() now returns parameters for unsupervised random forest when a single class response is specified.
Added miss_injections and batch_correction arguments to detectPretreatmentParameters() to specify if miss injection detection and/or batch correction detection is performed.
The RSDthresh parameter is now set by detectPretreatmentParameters() for the MetaboProfile S4 class depending on the technique used.
Miss injections are now detected below a percentage threshold of the median total ion count in detectMissInjections().
Added the isotopic_adducts argument to reduce() to allow the removal of m/z features assigned isotopic adducts.
The row order of the output of convertSampleInfo() will now always match the row order of the input.
Added the user_text argument to convertSampleInfo() to denote the column names for the User text fields.

exportCSV() now recursively creates the destination directory if it does not already exist.

detectPretreatmentParameters() now fully matches the QCidx argument against the supplied class information when detecting the presence of QC samples.

Corrected the exported file name for mode-less processed data for the MetaboProfile class.
Fixed the character sanitation in sanitiseTable().
Fixed extraneous console messages in detectMissInjections() and detectBatchDiff() methods for the MetaboProfile class.
Enabled unit tests for methods for the MetaboProfile class.
detectPretreatmentParameters() now detects the presence of QC samples.

Removed aberHRML/metaboData from the Remotes field in the DESCRIPTION to ensure that the CRAN version of metaboData is installed.
Added sanitiseTable() that can be used to restrict the number of rows in a table and round numeric columns to a given number of significant figures.

Fixed missing argument error in detectPretreatmentParameters() when miss injections are detected.

Added gzip_ext argument to convertSampleInfo() to enable the addition of the .gz file extension to file names in the fileNames column.

Added generic methods for exporting individual elements of the Binalysis, MetaboProfile, Analysis and Assignment classes.
export methods now return vectors of file paths of the exported files.

Added addAssignments() method for Analysis and Assignment classes.
Added exportCSV() that exports data to .csv format and returns the file path of the exported file.
Added convertSampleInfo() to convert sample information returned from grover::runInfo to a format compatible with the binneR and profilePro packages.

Added pkgdown site available here.
Removed redundant methods and functions: detectPairwises(), addAssignments(), filterCorrelations(), theme_neat().
Improved documentation and added examples.
Added unit testing infrastructure.
Added detectPretreatmentParameters and detectModellingParameters methods.
The magrittr pipe (%>%) is now re-exported.

Added metaboMisc::featureSummary() to summarise spectral features in the Binalysis S4 class.

Added a NEWS.md file to track changes to the package.
Added metaboMisc::suitableParallelPlan() to generate a suitable parallel processing future plan.