ExperimentalDesignFile Class Reference

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 )

staticprivate

load()

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

static

Loads an experimental design from a tabular separated file.

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  )

staticprivate

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  )

staticprivate

parseTwoTableFile_()

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

staticprivate