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| ExperimentalDesign ()=default |
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| ExperimentalDesign (const MSFileSection &msfile_section, const SampleSection &sample_section) |
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const MSFileSection & | getMSFileSection () const |
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void | setMSFileSection (const MSFileSection &msfile_section) |
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const ExperimentalDesign::SampleSection & | getSampleSection () const |
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void | setSampleSection (const SampleSection &sample_section) |
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std::map< std::vector< String >, std::set< unsigned > > | getUniqueSampleRowToSampleMapping () const |
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std::map< unsigned, unsigned > | getSampleToPrefractionationMapping () const |
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std::map< unsigned int, std::vector< String > > | getFractionToMSFilesMapping () const |
| return fraction index to file paths (ordered by fraction_group) More...
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std::vector< std::vector< std::pair< String, unsigned > > > | getConditionToPathLabelVector () const |
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std::map< std::vector< String >, std::set< unsigned > > | getConditionToSampleMapping () const |
| return a condition (unique combination of sample section values except replicate) to Sample index mapping More...
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std::map< std::pair< String, unsigned >, unsigned > | getPathLabelToPrefractionationMapping (bool use_basename_only) const |
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std::map< std::pair< String, unsigned >, unsigned > | getPathLabelToConditionMapping (bool use_basename_only) const |
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std::map< unsigned, unsigned > | getSampleToConditionMapping () const |
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std::map< std::pair< String, unsigned >, unsigned > | getPathLabelToSampleMapping (bool use_basename_only) const |
| return <file_path, label> to sample mapping More...
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std::map< std::pair< String, unsigned >, unsigned > | getPathLabelToFractionMapping (bool use_basename_only) const |
| return <file_path, label> to fraction mapping More...
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std::map< std::pair< String, unsigned >, unsigned > | getPathLabelToFractionGroupMapping (bool use_basename_only) const |
| return <file_path, label> to fraction_group mapping More...
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unsigned | getNumberOfSamples () const |
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unsigned | getNumberOfFractions () const |
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unsigned | getNumberOfLabels () const |
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unsigned | getNumberOfMSFiles () const |
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unsigned | getNumberOfFractionGroups () const |
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unsigned | getSample (unsigned fraction_group, unsigned label=1) |
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bool | isFractionated () const |
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bool | sameNrOfMSFilesPerFraction () const |
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Representation of an experimental design in OpenMS. Instances can be loaded with the ExperimentalDesignFile class.
Experimental designs can be provided in two formats: the one-table format and the two-table format.
The one-table format is simpler but slightly more redundant.
The one-table format consists of mandatory (file columns) and optional sample metadata (sample columns).
The mandatory file columns are Fraction_Group, Fraction, Spectra_Filepath and Label. These columns capture the mapping of quantitative values to files for label-free and multiplexed experiments and enables fraction-aware data processing.
- Fraction_Group: a numeric identifier that indicates which fractions are grouped together.
- Fraction: a numeric identifier that indicates which fraction was measured in this file. In the case of unfractionated data, the fraction identifier is 1 for all samples.
- Label: a numeric identifier for the label. 1 for label-free, 1 and 2 for SILAC light/heavy, e.g., 1-10 for TMT10Plex
- Spectra_Filepath: a filename or path as string representation (e.g., SILAC_file.mzML)
For processing with MSstats, the optional sample columns are typically MSstats_Condition and MSstats_BioReplicate with an additonal MSstats_Mixture column in the case of TMT labeling. They capture the experimental factors and conditions associated with a sample.
- MSstats_Condition: a string that indicates the condition (e.g. control or 1000 mMol). Will be forwarded to MSstats and can then be used to specify test contrasts.
- MSstats_BioReplicate: a numeric identifier to indicate replication. MSstats requires that there are no duplicate entries. E.g., if MSstats_Condition, Fraction_Group group, and Fraction number are the same - as in the case of biological or technical replication, one uses the MSstats_BioReplicate to make entries non-unique)
- MSstats_Mixture: (for TMT labeling only): a numeric identifier to indicate the mixture of samples labeled with different TMT reagents, which can be analyzed in a single mass spectrometry experiment. E.g., same samples labeled with different TMT reagents have a different mixture identifier. Technical replicates need to have the same mixture identifer.
For details on the MSstats columns please refer to the MSstats manual for details (https://www.bioconductor.org/packages/release/bioc/vignettes/MSstats/inst/doc/MSstats.html).
Fraction_Group | Fraction | Spectra_Filepath | Label | MSstats_Condition | MSstats_BioReplicate |
1 | 1 | UPS1_12500amol_R1.mzML | 1 | 12500 amol | 1 |
2 | 1 | UPS1_12500amol_R2.mzML | 1 | 12500 amol | 2 |
3 | 1 | UPS1_12500amol_R3.mzML | 1 | 12500 amol | 3 |
... | ...
| ... | ...
| ...
| ...
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22 | 1 | UPS1_500amol_R1.mzML | 1 | 500 amol | 1 |
23 | 1 | UPS1_500amol_R2.mzML | 1 | 500 amol | 2 |
24 | 1 | UPS1_500amol_R3.mzML | 1 | 500 amol | 3 |
Alternatively, the experimental design can be specified with a file consisting of two tables whose headers are separated by a blank line. The two tables are:
- The file section table and the sample section table.
- The file section consists of columns Fraction_Group, Fraction, Spectra_Filepath, Label and Sample
The sample section consists of columns Sample, MSstats_Condition and MSstats_BioReplicate.
The content is the same as described for the one table format, except that the additional numeric sample column allows referencing between file and sample section.
Fraction_Group | Fraction | Spectra_Filepath | Label | Sample |
1 | 1 | UPS1_12500amol_R1.mzML | 1 | 1 |
2 | 1 | UPS1_12500amol_R2.mzML | 1 | 2 |
... | ...
| ... | ...
| ...
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22 | 1 | UPS1_500amol_R1.mzML | 1 | 22 |
Sample | MSstats_Condition | MSstats_BioReplicate |
1 | 12500 amol | 1 |
2 | 12500 amol | 2 |
... | ...
| ...
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22 | 500 amol | 3 |