| OpenMS 2.5.0

Static Public Member Functions | Static Private Member Functions | List of all members
ExperimentalDesignFile Class Reference
Format

Provides means to load an ExperimentalDesign from a TSV file. More...

`#include <OpenMS/FORMAT/ExperimentalDesignFile.h>`

## Static Public Member Functions

static ExperimentalDesign | load (const String &tsv_file, bool require_spectra_files)
| Loads an experimental design from a tabular separated file. More...

## Static Private Member Functions

static bool | isOneTableFile_ (const TextFile &text_file)
static ExperimentalDesign | parseOneTableFile_ (const TextFile &text_file, const String &tsv_file, bool require_spectra_file)
static ExperimentalDesign | parseTwoTableFile_ (const TextFile &text_file, const String &tsv_file, bool require_spectra_file)
static void | parseHeader_ (const StringList &header, const String &filename, std::map< String, Size > &column_map, const std::set< String > &required, const std::set< String > &optional, bool allow_other_header)

## Detailed Description

Provides means to load an ExperimentalDesign from a TSV file.

1) Mandatory section with file-level information of the experimental design. Required to process fractionated data and multiplexed data.

File Section format:

Single header line Fraction_Group: Index used to group fractions and source files. Note: For label-free this has same cardinality as sample. For multiplexed experiments, these might differ as multiple samples can be measured in single files Fraction: 1st, 2nd, .., fraction. Note: All runs must have the same number of fractions. Spectra_Filepath: Path to mzML files Label: Label in MS file: label-free: always 1 TMT6Plex: 1..6 SILAC with light and heavy: 1..2 Sample: Index of sample measured in the specified label X, in fraction Y of fraction group Z

Fraction_Group Fraction Spectra_Filepath Label Sample 1 1 SPECTRAFILE_F1_TR1.mzML 1 1 1 2 SPECTRAFILE_F2_TR1.mzML 1 1 1 3 SPECTRAFILE_F3_TR1.mzML 1 1 1 1 SPECTRAFILE_F1_TR1.mzML 2 2 1 2 SPECTRAFILE_F2_TR1.mzML 2 2 1 3 SPECTRAFILE_F3_TR1.mzML 2 2 1 1 SPECTRAFILE_F1_TR1.mzML 3 3 1 2 SPECTRAFILE_F2_TR1.mzML 3 3 1 3 SPECTRAFILE_F3_TR1.mzML 3 3 1 1 SPECTRAFILE_F1_TR1.mzML 4 4 1 2 SPECTRAFILE_F2_TR1.mzML 4 4 1 3 SPECTRAFILE_F3_TR1.mzML 4 4 2 1 SPECTRAFILE_F1_TR2.mzML 1 5 2 2 SPECTRAFILE_F2_TR2.mzML 1 5 2 3 SPECTRAFILE_F3_TR2.mzML 1 5 2 1 SPECTRAFILE_F1_TR2.mzML 2 6 2 2 SPECTRAFILE_F2_TR2.mzML 2 6 2 3 SPECTRAFILE_F3_TR2.mzML 2 6 2 1 SPECTRAFILE_F1_TR2.mzML 3 7 2 2 SPECTRAFILE_F2_TR2.mzML 3 7 2 3 SPECTRAFILE_F3_TR2.mzML 3 7 2 1 SPECTRAFILE_F1_TR2.mzML 4 8 2 2 SPECTRAFILE_F2_TR2.mzML 4 8 2 3 SPECTRAFILE_F3_TR2.mzML 4 8

2) Mandatory section with sample information of the experimental design. One Column must be 'Sample', other columns are unspecified and can contain arbitrary factors

Sample Some_Condition1 Some_Condition2 1 1 1 2 2 1 3 3 1 4 4 1 5 1 2 6 2 2 7 3 2 8 4 2

## Member Function Documentation

## ◆ isOneTableFile_()

static bool isOneTableFile_ | ( | const TextFile & | text_file | ) |

static private

## ◆ load()

static ExperimentalDesign load | ( | const String & | tsv_file,
|  | bool | require_spectra_files
| ) |  |

static

Loads an experimental design from a tabular separated file.

Referenced by UTILProteomicsLFQ::main_().

## ◆ parseHeader_()

static void parseHeader_ | ( | const StringList & | header,
|  | const String & | filename,
|  | std::map< String, Size > & | column_map,
|  | const std::set< String > & | required,
|  | const std::set< String > & | optional,
|  | bool | allow_other_header
| ) |  |

static private

Reads header line of File and Sample section, checks for the existence of required headers and maps the column name to its position

## ◆ parseOneTableFile_()

static ExperimentalDesign parseOneTableFile_ | ( | const TextFile & | text_file,
|  | const String & | tsv_file,
|  | bool | require_spectra_file
| ) |  |

static private

## ◆ parseTwoTableFile_()

static ExperimentalDesign parseTwoTableFile_ | ( | const TextFile & | text_file,
|  | const String & | tsv_file,
|  | bool | require_spectra_file
| ) |  |

static private