Filter workflow4metabolomics XCMS datasets by metadata or intensity

The w4mclassfilter R package provides the computational back-end of a Galaxy tool for inclusion in Workflow4Metabolomics (W4M).

This package (and the corresponding Galaxy tool) perform several steps,
either to reduce the number samples or features to be analyzed,
or to address several data issues that may impede downstream statistical analysis:

• Samples that are missing from either sampleMetadata or dataMatrix are eliminated.
• Samples may also be eliminated by a "sample class" column in sampleMetadata.
• Features that are missing from either variableMetadata or dataMatrix are eliminated.
• Features may be eliminated by specifying minimum or maximum value (or both) allowable in columns of variableMetadata.
• Features may be eliminated by specifying minimum or maximum intensity (or both) allowable in columns of dataMatrix for at least one sample for each feature ("range of row-maximum for each feature").
• Missing values in dataMatrix are imputed either to zero (by default) or to the result of a user-supplied imputation function.
• Features and samples that have zero variance are eliminated.
• Samples and features are sorted alphabetically in rows and columns of variableMetadata, sampleMetadata, and dataMatrix
• By default, the names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata"

Changes in version 0.98.7

New Features

• First column of sample metadata is by default renamed to "sampleMetadata" unless argument 'name_smplmetadata_col1' is supplied and set to FALSE.

Internal Modifications

• none

w4mclassfilter Release v0.98.6

Changes in version 0.98.6

SIGNIFICANT USER-VISIBLE CHANGES

• Support eliminating features whose attributes fall outside specified ranges.
• Sort sample names and feature names because some statistical tools expect the same order in dataMatrix row and column names as in the corresponding metadata files.

OTHER

• Support and tests for new features.

w4mclassfilter Release v0.98.3

NEW FEATURES

• Added support for working with XCMS in R outside the context of Galaxy Workflow4Metabolomics.

INTERNAL MODIFICATIONS

• Support and tests for new features.

BUILD NOTES

• This package was built with R 3.3.1 under miniconda as follows:

~/src/w4mclassfilter$ ~/miniconda2/bin/conda create -n r3.4.1 r-base=3.4.1
~/src/w4mclassfilter$ source ~/miniconda2/bin/activate r3.4.1
(r3.4.1) $ R

library(devtools)
document()
rmarkdown::render("vignettes/w4mclassfilter.Rmd", "all")
test()
check()
build()
install()

Result is at ~/src/w4mclassfilter_0.98.3.tar.gz

w4mclassfilter Release v0.98.2

CHANGES IN VERSION 0.98.2

NEW FEATURES

• Added support for R-flavored regular expression pattern matching.
• Empty classes argument or zero-length class_column result in no samples filtered out.

INTERNAL MODIFICATIONS

• Support and tests for new features.

BUILD NOTES

• This package was built with R 3.3.1 under miniconda as follows:

  ~/src/w4mclassfilter$ ~/miniconda2/bin/conda create -n r3.3.1 r-base=3.3.1
  ~/src/w4mclassfilter$ source ~/miniconda2/bin/activate r3.3.1
  (r3.3.1) $ R
  > library(devtools)
  > document()
  > test()
  > check()
  > build()
  > install()

Result is at ~/src/w4mclassfilter_0.98.2.tar.gz

w4mclassfilter Release v0.98.1

Second release - R package that implements flitering of W4M data matrix and metadata by class of sample.
Improves documentation and fixes bugs (albeit undocumented bugs).

I have not yet evaluated the integrity of this release - the unit tests pass, however.

w4mclassfilter Release v0.98.0

First release - R package that implements flitering of W4M data matrix and metadata by class of sample.