NEWS.md

In jasenfinch/metaboMisc: Miscellaneous Functions for Metabolomics Analyses

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.

metaboMisc 0.6.3

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

metaboMisc 0.6.2

• 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.

metaboMisc 0.6.1

• Fix the missing name column in tables returned from convertSampleInfo().

metaboMisc 0.6.0

• 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.

metaboMisc 0.5.11

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

metaboMisc 0.5.10

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

metaboMisc 0.5.9

• 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.

metaboMisc 0.5.8

• Numbers of characters in strings are now limited by sanitiseTable().

metaboMisc 0.5.7

• 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.

metaboMisc 0.5.6

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

metaboMisc 0.5.5

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

metaboMisc 0.5.4

• Added exportModelling() method for the Analysis class.

metaboMisc 0.5.3

• 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.

metaboMisc 0.5.2

• 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.

metaboMisc 0.5.1

• Fixed error in detectPretreatmentParameters().

metaboMisc 0.5.0

• 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.

metaboMisc 0.4.6

• Fixed parameter handling in preTreatModes.

metaboMisc 0.4.5

• Fixed breakages and function imports caused by metabolyseR to version 0.14.0.

metaboMisc 0.4.4

• Fixed binneR::sampleInfo() imports with binneR v2.5.0 update.

metaboMisc 0.4.3

• Fixed missing method exports for metaboMisc::addAssignments(), metaboMisc::detectBatchDiff(), metaboMisc::detectMissInjections(), metaboMisc::detectPairwises() and metaboMisc::reduce().

metaboMisc 0.4.2

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

metaboMisc 0.4.1

• Added a NEWS.md file to track changes to the package.

• Added metaboMisc::suitableParallelPlan() to generate a suitable parallel processing future plan.

jasenfinch/metaboMisc documentation built on July 31, 2023, 2:28 a.m.