Filter workflow4metabolomics XCMS datasets by metadata or intensity

The w4mclassfilter R package provides the computational back-end of a Galaxy tool to complement 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 have consistent order in variableMetadata, sampleMetadata, and dataMatrix.
  • The column(s) for sorting variableMetadata or sampleMetadata may be specified or defaults to the first column.
• By default, the names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata"
• An advanced option enables producing a "center" for each treatment in lieu of the samples for each treatment.

Changes in version 0.98.19

SIGNIFICANT USER-VISIBLE CHANGES

• Bug fix #9 - "medoid computation aborts when trt is numeric or some trts have one replicate"

INTERNAL CHANGES

• Built with R 4.0.3 (2020-10-10) "Bunny-Wunnies Freak Out"
• Built with the command R CMD build w4mclassfilter to assure that vignettes are built as intended.

HASH

• sha256sum of w4mclassfilter_0.98.19.tar.gz - 64a0dca07a3daea4f193355d4a69c568a0f7bf8358445849e269ecd1b3efed48

Filter workflow4metabolomics XCMS datasets by metadata or intensity

The w4mclassfilter R package provides the computational back-end of a Galaxy tool to complement 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 have consistent order in variableMetadata, sampleMetadata, and dataMatrix.
  • The column(s) for sorting variableMetadata or sampleMetadata may be specified or defaults to the first column.
• By default, the names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata"
• An advanced option enables producing a "center" for each treatment in lieu of the samples for each treatment.

Changes in version 0.98.18

SIGNIFICANT USER-VISIBLE CHANGES

• Bug fix #8 - "centroid and median computation fails for some inputs"

INTERNAL CHANGES

• Built with R 3.6.2 (2019-12-12) "Dark and Stormy Night"
• Built with the command R CMD build w4mclassfilter to assure that vignettes are built as intended.

HASH

• sha256sum of w4mclassfilter_0.98.18.tar.gz - 4dcba3efed6816032cc233a0e85fefe4576735d231803d73bb3285b322b8f4ef

Filter workflow4metabolomics XCMS datasets by metadata or intensity

The w4mclassfilter R package provides the computational back-end of a Galaxy tool to complement 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 have consistent order in variableMetadata, sampleMetadata, and dataMatrix.
  • The column(s) for sorting variableMetadata or sampleMetadata may be specified or defaults to the first column.
• By default, the names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata"
• An advanced option enables producing a "center" for each treatment in lieu of the samples for each treatment.

Changes in version 0.98.17

NEW FEATURES

• Enhancement #7 - "enable sorting on multiple columns of metadata"

HASH

• sha256sum of w4mclassfilter_0.98.17.tar.gz - 66c7e63d3d2603f433883369b4497e9665fff42b636c5f73c905fdd037f42079

Filter workflow4metabolomics XCMS datasets by metadata or intensity

The w4mclassfilter R package provides the computational back-end of a Galaxy tool to complement 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 have consistent order in variableMetadata, sampleMetadata, and dataMatrix.
  • The column for sorting variableMetadata or sampleMetadata may be specified or defaults to the first column.
• By default, the names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata"
• An advanced option enables producing a "center" for each treatment in lieu of the samples for each treatment.

Changes in version 0.98.16

NEW FEATURES

• None (apart from documentation changes).

INTERNAL MODIFICATIONS

• Corrected internal calculation of medoids (to use principal-component scores as coordinates for distance calculations). See #6 (comment) for details.
• Built with R 3.6.1 (2019-07-05) "Action of the Toes"

Filter workflow4metabolomics XCMS datasets by metadata or intensity

The w4mclassfilter R package provides the computational back-end of a Galaxy tool to complement 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 have consistent order in variableMetadata, sampleMetadata, and dataMatrix.
  • The column for sorting variableMetadata or sampleMetadata may be specified or defaults to the first column.
• By default, the names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata"
• An advanced option enables producing a "center" for each treatment in lieu of the samples for each treatment.

Changes in version 0.98.15

NEW FEATURES

• Enhancement #6 - "compute center for each treatment"

INTERNAL MODIFICATIONS

• Built with R 3.6.1 (2019-07-05) "Action of the Toes"
• Built with the command R CMD build w4mclassfilter to assure that vignettes are built as intended.

Filter workflow4metabolomics XCMS datasets by metadata or intensity

The w4mclassfilter R package provides the computational back-end of a Galaxy tool to complement 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 have consistent order in variableMetadata, sampleMetadata, and dataMatrix.
  • The column for sorting variableMetadata or sampleMetadata may be specified or defaults to the first column.
• By default, the names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata"

Changes in version 0.98.14

NEW FEATURES

• Enhancement HegemanLab/w4mclassfilter_galaxy_wrapper#6 - "Provide sort options for features and samples"

INTERNAL MODIFICATIONS

• Built with R 3.6.1 (2019-07-05) "Action of the Toes"

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 0.98.13

NEW FEATURES

• none

INTERNAL MODIFICATIONS

• Fix issue #5 - "MAXFEAT does not work for imputation functions that include data transformation"
• Built with R 3.6.1 (2019-07-05) "Action of the Toes"

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 0.98.12

CHANGES IN VERSION 0.98.12

NEW FEATURES

• Enhancement #4 - "add and test no-imputation and centering-imputation functions":
  • Support no imputation.
  • Support imputating missing feature-intensities as median intensity for the corresponding feature.

INTERNAL MODIFICATIONS

• Support and tests for new features.
• Built with R 3.6.1 (2019-07-05) "Action of the Toes"
• Version numbers 0.98.10 and 0.98.11 were skipped to synchronize with w4mclassfilter_galaxy_wrapper

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 0.98.9

New features

• none

Internal modifications

• Fix #3 -
  "a single column is insufficient to calculate a variance"
• Built with R version 3.4.1 (2017-06-30) "Single Candle"

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 0.98.8

New features

• none

Internal modifications

• Fix #1 - "bad error handling when input file cannot be found"
• Add tests for missing and invalid input files
• Built with R version 3.4.1 (2017-06-30) "Single Candle"