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Public Member Functions | Protected Member Functions | Protected Attributes

ms_ms2quantitation Class Reference
[Quantitation analysis for Mascot Server and Distiller]

Peptide and protein quantitation in a Reporter or Multiplex Mascot results file. More...

#include <ms_ms2quantitation.hpp>

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List of all members.

Public Member Functions

 ms_ms2quantitation (const ms_peptidesummary &pepsum)
 Default constructor: load the quantitation method from the results file and quantitate all peptides that pass the quality thresholds.
 ms_ms2quantitation (const ms_peptidesummary &pepsum, const ms_quant_method &qm)
 Quantitate all peptides that pass the quality thresholds using the given quantitation method.
virtual ~ms_ms2quantitation ()
 Destructor.
void appendErrors (const ms_errors &src)
 Copies all errors from another instance and appends them at the end of own list.
void clearAllErrors ()
 Remove all errors from the current list of errors.
void copyFrom (const ms_errors *right)
 Use this member to make a copy of another instance.
const ms_quant_ratiogetCombinedReportRatio (const std::string &ratioName) const
 Return a combined quantitation ratio matching the given name.
std::vector< std::string > getCombinedReportRatioNames () const
 Return a list of current combined report ratio names.
std::vector< double > getComponentIntensities (const ms_peptide_quant_key &key, bool raw=false) const
 Return the component intensities for the given peptide-spectrum match, if available.
const ms_errsgetErrorHandler () const
 Retrive the error object using this function to get access to all errors and error parameters.
double getIntensityNormalisationBase (const std::string &componentName) const
 Get the intensity normalisation base of the given component name.
int getLastError () const
 Return the error description of the last error that occurred.
std::string getLastErrorString () const
 Return the error description of the last error that occurred.
ms_peptide_quant_key_vector getPeptideQuantKeys (const std::string &accession, int dbIdx) const
 Look up peptide quant keys associated with a given protein, if any.
virtual ms_peptide_quant_ratio getPeptideRatio (const ms_peptide_quant_key &key, const std::string &ratioName) const
 Given peptide quant key and ratio name, return the corresponding peptide ratio data.
double getPeptideRatioNormalisationBase (const std::string &ratioName) const
 Get the peptide ratio normalisation base of the given ratio name.
virtual ms_protein_quant_ratio getProteinRatio (const std::string &accession, int dbIdx, const std::string &ratioName) const
 Given the protein accession, database ID and ratio name, return the protein ratio data.
virtual ms_protein_quant_ratio getProteinRatio (const std::string &accession, int dbIdx, const std::string &ratioName, const ms_peptide_quant_key_vector &includeKeys, const ms_peptide_quant_key_vector &excludeKeys) const
 Given the protein accession, database ID and ratio name, return the protein ratio data, overriding the default inclusion and exclusion of the specified peptide quant keys.
const ms_quant_methodgetQuantitationMethod () const
 Return the current quantitation method.
const ms_quant_ratiogetReportRatioFromFile (unsigned int fileNum, const std::string &ratioName) const
 Return a quantitation ratio matching the given name in the given file.
std::vector< std::string > getReportRatioNamesInFile (unsigned int fileNum) const
 Return a list of current report ratio names in the given file.
bool hasIntensityNormalisation () const
 Return true if intensity normalisation is enabled and configured.
virtual bool hasPeptideRatio (const ms_peptide_quant_key &key, const std::string &ratioName) const
 Existence check: return true if a peptide ratio with the associated peptide quant key and ratio name exists.
bool hasPeptideRatioNormalisation () const
 Return true if peptide ratio normalisation is enabled and configured.
virtual bool isPeptideRatioExcluded (const ms_peptide_quant_key &key, const std::string &ratioName) const
 Boolean flag: is the given peptide ratio globally excluded from protein ratio calculation?
bool isValid () const
 Call this function to determine if there have been any errors.
void normaliseIntensities ()
 Normalise component intensities, or do nothing if intensity normalisation is disabled.
void normalisePeptideRatios ()
 Normalise peptide ratios, or do nothing if normalisation is disabled.
void removeCombinedReportRatio (const std::string &ratioName)
 Remove the combined quantitation ratio matching the given name from all files.
void removeIntensityNormalisationBase (const std::string &componentName)
 Reset the intensity normalisation base of the given ratio name.
void removeIntensityNormalisationBases ()
 Reset all Intensity normalisation bases.
void removePeptideRatioNormalisationBase (const std::string &ratioName)
 Reset the peptide ratio normalisation base of the given ratio name.
void removePeptideRatioNormalisationBases ()
 Reset all peptide ratio normalisation bases.
void removeReportRatioInFile (unsigned int fileNum, const std::string &ratioName)
 Remove the quantitation ratio matching the given name from the given file.
void setCombinedReportRatio (const std::string &ratioName, const ms_quant_ratio &ratioDef)
 Add or modify the combined quantitation ratio matching the given name in all files.
void setIntensityNormalisationBase (const std::string &componentName, double b)
 Set the intensity normalisation base of the given component name.
void setMinNumPeptides (int value)
 Set the minimum number of peptides needed for protein ratio calculation.
virtual void setPeptideRatioExcluded (const ms_peptide_quant_key &key, const std::string &ratioName)
 Globally exclude a particular peptide ratio from protein ratio calculation.
virtual void setPeptideRatioIncluded (const ms_peptide_quant_key &key, const std::string &ratioName)
 Globally include a particular peptide ratio in protein ratio calculation.
void setPeptideRatioNormalisationBase (const std::string &ratioName, double b)
 Set the peptide ratio normalisation base of the given ratio name.
virtual void setProteinRatioType (const char *value)
 Set the protein ratio type.
void setQuantNormalisation (const ms_quant_normalisation *norm)
 Set new peptide and protein ratio normalisation settings.
virtual void setQuantOutliers (const ms_quant_outliers *)
 Set new peptide ratio outlier settings.
void setReportRatioInFile (unsigned int fileNum, const std::string &ratioName, const ms_quant_ratio &ratioDef)
 Add or modify the quantitation ratio matching the given name in the given file.

Protected Member Functions

ms_protein_quant_ratio calculateGeometricMeanRatio (const std::string &accession, int dbIdx, const std::string &ratioName, const std::vector< double > &sample, const std::vector< double > &logSample, const std::vector< ms_peptide_quant_key > &activeKeys, const std::map< ms_peptide_quant_key, int > &inactiveKeys, double normalityPvalue) const
 Given a sample of peptide ratios, calculate the geometric mean and standard deviation.
ms_protein_quant_ratio calculateMedianRatio (const std::string &accession, int dbIdx, const std::string &ratioName, const std::vector< double > &sample, const std::vector< double > &logSample, const std::vector< ms_peptide_quant_key > &activeKeys, const std::map< ms_peptide_quant_key, int > &inactiveKeys, double normalityPvalue) const
 Given a sample of peptide ratios, calculate the median and standard deviation from the median.
ms_protein_quant_ratio calculateWeightedGeometricMeanRatio (const std::string &accession, int dbIdx, const std::string &ratioName, const std::vector< double > &sample, const std::vector< double > &logSample, const std::vector< double > &weights, const std::vector< ms_peptide_quant_key > &activeKeys, const std::map< ms_peptide_quant_key, int > &inactiveKeys, double normalityPvalue) const
 Given a sample of peptide ratios, calculate the weighted geometric mean and standard deviation.
virtual int countDistinctPeptides (const std::vector< ms_peptide_quant_key > &activeKeys) const
int getMinNumPeptides () const
 Get the minimum number of peptides needed for protein ratio calculation.
void getProteinRatioSample (const std::string &accession, int dbIdx, const std::string &ratioName, const std::vector< ms_peptide_quant_key > &includeKeys, const std::vector< ms_peptide_quant_key > &excludeKeys, std::vector< double > &sample, std::vector< double > &logSample, std::vector< double > &weights, std::vector< ms_peptide_quant_key > &activeKeys, std::map< ms_peptide_quant_key, int > &inactiveKeys, double &normalityPvalue) const
 Find the peptide quant keys associated with the protein, collect their unique peptide ratios, remove outliers (if desired) and return the values as the sample of peptide ratios.
virtual void getSortedFinitePeptideRatioValues (const std::string &ratioName, const std::set< ms_peptide_quant_key > &keys, const std::set< ms_peptide_quant_key > &includeKeys, const std::set< ms_peptide_quant_key > &excludeKEys, std::vector< double > &values, std::vector< double > &weights, std::vector< ms_peptide_quant_key > &activeKeys, std::map< ms_peptide_quant_key, int > &inactiveKeys) const
 Given a list of q,p values and ratio name, find the non-infinite peptide ratio values and return them in numerically increasing order.
bool initialiseBaseSettings (const ms_quant_method &qmBase, const ms_quant_method &qmConfig)
 Initialise quantitation method settings from the two method objects.

Protected Attributes

protein_to_peptide_quant_key_t proteinKeys_
 < Protein-to-peptide mapping.

Detailed Description

Peptide and protein quantitation in a Reporter or Multiplex Mascot results file.

ms_ms2quantitation implements a single use case: given a Mascot results file of a search whose quantitation protocol is Reporter (e.g. iTRAQ) or Multiplex (e.g. 18O), it will calculate, on demand, peptide and proteins ratios from component intensities extracted from the MS/MS spectra.

Peptide ratios are identified by q,p peptide quant keys (ms_peptide_quant_key(int q, int p)). Not all peptide matches in the results file have an associated peptide ratio; for example, the Reporter ions could be missing from the input query.

Protein ratios are identified by protein accession and database index. There are three types of ratio: median, average and weighted. Median is the median of all peptide ratios associated with the protein hit, and average is the geometric mean (equivalently, the arithmetic mean of log-transformed peptide ratios). Weighted is a weighted mean of peptide ratios, where the weights are channel intensities. The weighted ratio type is only available for Reporter data.

All values are read-only. If you need to edit anything, apart from protein ratio calculation settings, or if you need to use some other protocol, use ms_customquantitation instead.

The class supports all types of normalisation configurable in the quantitation method. However, you need to explicitly ask for the normalisation constants to be calculated (see normalisePeptideRatios()). This is because normalisation may require calculating peptide ratios for all quantifiable peptide matches in the results file, which can be a time-consuming operation. Thus, if you change parameters or ratio definitions, and normalisation is enabled, you will need to call normalisePeptideRatios() to recalculate the normalisation constants. (If normalisation is not enabled, there is no penalty in calling normalisePeptideRatios().)

You can skip the remainder of this section if you are not combining results files (see Combining multiple .dat files for background reading).

If the results file is a merged file, peptide ratios will be merged across the files in the following way. Imagine peptide ratios are arranged in a table, so that a row contains the report ratios for a particular peptide (q,p), and the columns are indexed by report ratio names. Each report ratio with a unique name becomes its own column. If a report ratio with the same name appears in more than one file, these are treated as the same column (regardless of whether the formulas are exactly the same).

There are three complications which you must address:

  1. Two report ratios with the same formula may not actually have the same name in different files (e.g. the iTRAQ 115/114 ratio is called "115/114" in one file but "Control" in another).
  2. Two report ratios with the same name may not actually have the same formulas in different files (e.g. the report ratio named "Control" in one file is not calculated the same way "Control" is in another).
  3. Two report ratios with the same name and same formula may mean different things in different files (e.g. "115/114" is control in one file, patient in another).

The solution is to modify report ratios in different files using setCombinedReportRatio(), so that the names, formulas and meanings match between files. Of course, if you want to keep ratios from different files separate, you need to rename ratios in each file (using setReportRatioInFile()) so that they are all different across all files.

Note the naming convention: methods with "InFile" (e.g. setReportRatioInFile()) modify report ratios in a single file (in the combined results file), while methods with "Combined" (e.g. setCombinedReportRatio()) modify report ratios across all files (in the combined results file).


Constructor & Destructor Documentation

ms_ms2quantitation ( const ms_peptidesummary pepsum ) [explicit]

Default constructor: load the quantitation method from the results file and quantitate all peptides that pass the quality thresholds.

The constructor performs the following steps. If any of them fail, the corresponding error will be set and the object left in invalid state. Use isValid() to check for this and getLastErrorString() to fetch the error description:

  • Load the quantitation method from the results file. If the results file has no quantitation method, or it doesn't validate against the schema, the process ends here.
  • If protocol isn't Reporter or Multiplex, the process ends here. (Use ms_customquantitation instead, as outlined in Peptide and protein quantitation.)
  • Prepare combined report ratios, if the input file is a combined results file.

Note that the constructor will not normalise peptide ratios or component intensities automatically, even if normalisation is enabled and configured. You need to call normalisePeptideRatios() and normaliseIntensities().

Parameters:
pepsumMascot results file to quantitate. Note that you must first validate the embedded XML sections of the results file. Either pass the schema directory to the ms_mascotresfile constructor or use ms_mascotresfile::setXMLschemaFilePath().
ms_ms2quantitation ( const ms_peptidesummary pepsum,
const ms_quant_method qm 
)

Quantitate all peptides that pass the quality thresholds using the given quantitation method.

The constructor performs the following steps. If any of them fail, the corresponding error will be set and the object left in invalid state. Use isValid() to check for this and getLastErrorString() to fetch the error description:

  • Load the quantitation method from the results file. If the results file has no quantitation method, or it doesn't validate against the default quantitation schema, the process ends here.
  • If protocol isn't Reporter or Multiplex, the process ends here. (Use ms_customquantitation instead, as outlined in Peptide and protein quantitation.)
  • If the protocol or component definitions between the embedded quantitation method and qm do not match, as tested with ms_quant_method::isMethodCompatible(), the process ends here with an error.
  • Prepare combined report ratios, if the input file is a combined results file.

Note that the constructor will not normalise peptide ratios or component intensities automatically, even if normalisation is enabled and configured. You need to call normalisePeptideRatios() and normaliseIntensities().

Parameters:
pepsumMascot results file to quantitate. Note that you must first validate the embedded XML sections of the results file. Either pass the schema directory to the ms_mascotresfile constructor or use ms_mascotresfile::setXMLschemaFilePath().
qmQuantitation method to use. The protocol and component definitions must match exactly those defined in the results file. It is best to use the return value from ms_mascotresfile::getQuantitationMethod() as the base and then alter peptide quality settings as needed.

Member Function Documentation

void appendErrors ( const ms_errors src ) [inherited]

Copies all errors from another instance and appends them at the end of own list.

Parameters:
srcThe object to copy the errors across from. See Maintaining object references: two rules of thumb.
ms_protein_quant_ratio calculateGeometricMeanRatio ( const std::string &  accession,
int  dbIdx,
const std::string &  ratioName,
const std::vector< double > &  sample,
const std::vector< double > &  logSample,
const std::vector< ms_peptide_quant_key > &  activeKeys,
const std::map< ms_peptide_quant_key, int > &  inactiveKeys,
double  normalityPvalue 
) const [protected, inherited]

Given a sample of peptide ratios, calculate the geometric mean and standard deviation.

Parameters:
accessionProtein accession. This is returned verbatim in the returned object and not used otherwise.
dbIdxProtein database index. This is returned verbatim in the returned object and not used otherwise.
ratioNameRatio name. This is returned verbatim in the returned object and not used otherwise.
sampleSample of peptide ratios in increasing numerical order. Sample size must be at least 1.
logSampleLog transform of sample.
normalityPvalueThe p-value that logSample looks normally distributed.
activeKeysPeptide quant keys for which sample values are present.
inactiveKeysPeptide quant keys ignored due to being skipped, excluded or detected as outliers.
Returns:
A protein ratio object encapsulating the calculated ratio, standard deviation and p-value, if relevant.
ms_protein_quant_ratio calculateMedianRatio ( const std::string &  accession,
int  dbIdx,
const std::string &  ratioName,
const std::vector< double > &  sample,
const std::vector< double > &  logSample,
const std::vector< ms_peptide_quant_key > &  activeKeys,
const std::map< ms_peptide_quant_key, int > &  inactiveKeys,
double  normalityPvalue 
) const [protected, inherited]

Given a sample of peptide ratios, calculate the median and standard deviation from the median.

See ms_quant_stats::sortedMedian for details of how this is calculated.

Parameters:
accessionProtein accession. This is returned verbatim in the returned object and not used otherwise.
dbIdxProtein database index. This is returned verbatim in the returned object and not used otherwise.
ratioNameRatio name. This is returned verbatim in the returned object and not used otherwise.
sampleSample of peptide ratios in increasing numerical order. Sample size must be at least 1.
logSampleLog transform of sample.
normalityPvalueThe p-value that logSample looks normally distributed.
activeKeysPeptide quant keys for which sample values are present.
inactiveKeysPeptide quant keys ignored due to being skipped, excluded or detected as outliers.
Returns:
A protein ratio object encapsulating the calculated ratio, standard deviation and p-values, if relevant.
ms_protein_quant_ratio calculateWeightedGeometricMeanRatio ( const std::string &  accession,
int  dbIdx,
const std::string &  ratioName,
const std::vector< double > &  sample,
const std::vector< double > &  logSample,
const std::vector< double > &  weights,
const std::vector< ms_peptide_quant_key > &  activeKeys,
const std::map< ms_peptide_quant_key, int > &  inactiveKeys,
double  normalityPvalue 
) const [protected, inherited]

Given a sample of peptide ratios, calculate the weighted geometric mean and standard deviation.

Parameters:
accessionProtein accession. This is returned verbatim in the returned object and not used otherwise.
dbIdxProtein database index. This is returned verbatim in the returned object and not used otherwise.
ratioNameRatio name. This is returned verbatim in the returned object and not used otherwise.
sampleSample of peptide ratios in increasing numerical order. Sample size must be at least 1.
logSampleLog transform of sample.
weightsWeighting factors corresponding to the order of sample (and logSample).
normalityPvalueThe p-value that logSample looks normally distributed.
activeKeysPeptide quant keys for which sample values are present.
inactiveKeysPeptide quant keys ignored due to being skipped, excluded or detected as outliers.
Returns:
A protein ratio object encapsulating the calculated ratio, standard deviation and p-value, if relevant.
void clearAllErrors (  ) [inherited]

Remove all errors from the current list of errors.

The list of 'errors' can include fatal errors, warning messages, information messages and different levels of debugging messages.

All messages are accumulated into a list in this object, until clearAllErrors() is called.

See Error Handling.

See also:
isValid(), getLastError(), getLastErrorString(), getErrorHandler()
Examples:
common_error.cpp, resfile_error.cpp, and resfile_summary.cpp.
void copyFrom ( const ms_errors right ) [inherited]

Use this member to make a copy of another instance.

Parameters:
rightis the source to initialise from
int countDistinctPeptides ( const std::vector< ms_peptide_quant_key > &  activeKeys ) const [protected, virtual]

The base class ms_quantitation does not have enough infomation about the peptides associated with each ms_peptide_quant_key to determine if they are truly distinct. By default, the number of distinct peptides is the number of elements in activeKeys.

In ms_ms1quantitation and ms_ms2quantitation, peptides are treated as distinctly different only if they have a difference in their peptide string.

Parameters:
activeKeysPeptide quant keys that are included in the quantitation of a protein.
Returns:
The number of distinct peptides.

Reimplemented from ms_quantitation.

const ms_quant_ratio * getCombinedReportRatio ( const std::string &  ratioName ) const

Return a combined quantitation ratio matching the given name.

Even if the report ratio formulas of ratio ratioName differ between the files, they are considered the same (merged in the same "column"), since they have the same name. This method returns the ratio definition from the first file (in numerical order) that has a definition with the name ratioName. You should always verify, using getReportRatioFromFile() and related methods, that the definitions with the same names are actually the same before relying on the return value of this method.

Parameters:
ratioNameThe name of the report ratio. This must match exactly (case sensitively) the desired report ratio name.
Returns:
If no such report ratio exists, this method returns NULL. Otherwise the corresponding object is returned.
std::vector< std::string > getCombinedReportRatioNames (  ) const

Return a list of current combined report ratio names.

This method returns the unique report ratio names across all files (i.e. the "columns" in the peptide ratio table).

Returns:
The list of combined report ratio names in the order they appear in each file. Duplicate ratio names are removed.
std::vector< double > getComponentIntensities ( const ms_peptide_quant_key key,
bool  raw = false 
) const

Return the component intensities for the given peptide-spectrum match, if available.

In the Reporter protocol, component intensities are extracted from a given input spectrum q based on the presence of reporter ion peaks, regardless of which peptide was matched to the spectrum. In this case all peptide matches in the same query that pass the quality threshold will have the same component intensities.

In the Multiplex protocol, component intensity extraction requires both the input spectrum q and the peptide that was matched to it, identified by (q,p). In this case, if component intensity extraction succeeded, then you may get different component intensities (or none at all) for different values of p.

Parameters:
keyPeptide quant key created with ms_peptide_quant_key(int q, int p).
raw(optional) If true, return raw intensities. Corrected intensities are returned by default. Note that if Reporter "sum" normalisation is in use, the corrected intensities will be normalised, whereas the raw intensities will not be.
Returns:
A vector of component intensities, in the same order as components are defined in the quantitation method. This can be empty if there is no component intensity data for the peptide-spectrum match or if it did not pass the quality thresholds.
const ms_errs * getErrorHandler (  ) const [inherited]

Retrive the error object using this function to get access to all errors and error parameters.

See Error Handling.

Returns:
Constant pointer to the error handler
See also:
isValid(), getLastError(), getLastErrorString(), clearAllErrors(), getErrorHandler()
Examples:
common_error.cpp, and http_helper_getstring.cpp.
double getIntensityNormalisationBase ( const std::string &  componentName ) const

Get the intensity normalisation base of the given component name.

Parameters:
componentNameName of one of the components defined in the quantitation method.
Returns:
The current intensity normalisation base, or 1 if it hasn't been set.
int getLastError (  ) const [inherited]

Return the error description of the last error that occurred.

All errors are accumulated into a list in this object, until clearAllErrors() is called. This function returns the last error that occurred.

See Error Handling.

See also:
isValid(), getLastErrorString(), clearAllErrors(), getErrorHandler()
Returns:
the error number of the last error, or 0 if there have been no errors.

Reimplemented in ms_mascotresfile.

std::string getLastErrorString (  ) const [inherited]

Return the error description of the last error that occurred.

All errors are accumulated into a list in this object, until clearAllErrors() is called. This function returns the last error that occurred.

Returns:
Most recent error, warning, information or debug message

See Error Handling.

See also:
isValid(), getLastError(), clearAllErrors(), getErrorHandler()

Reimplemented in ms_mascotresfile.

Examples:
common_error.cpp, config_enzymes.cpp, config_fragrules.cpp, config_license.cpp, config_mascotdat.cpp, config_masses.cpp, config_modfile.cpp, config_procs.cpp, config_quantitation.cpp, config_taxonomy.cpp, http_helper_getstring.cpp, and tools_aahelper.cpp.
int getMinNumPeptides (  ) const [protected, inherited]

Get the minimum number of peptides needed for protein ratio calculation.

Returns:
The minimum number of peptides needed for protein ratio calculation.
ms_peptide_quant_key_vector getPeptideQuantKeys ( const std::string &  accession,
int  dbIdx 
) const [inherited]

Look up peptide quant keys associated with a given protein, if any.

In ms_ms2quantitation, the list of peptide quant keys associated with the given protein is immutable, as the keys are derived from q,p values in the Mascot results file. The list does not contain all q,p values, but only those that 1) have component intensities and 2) pass the quality thresholds. Unless the data quality is extremely good, this list will always have fewer elements than the actual peptide matches assigned to the protein hit.

In ms_customquantitation, the peptide-to-protein mapping can be altered with ms_customquantitation::addPeptideQuantKey() and ms_customquantitation::removePeptideQuantKey().

Parameters:
accessionThe protein accession.
dbIdxThe protein database index.
Returns:
A vector of peptide quant keys associated with the protein.
ms_peptide_quant_ratio getPeptideRatio ( const ms_peptide_quant_key key,
const std::string &  ratioName 
) const [virtual]

Given peptide quant key and ratio name, return the corresponding peptide ratio data.

Often, most peptide matches in a Mascot results file have no ratio data. For example, the peptide match could be non-significant or not quantitable (quality check fails); or with Reporter or Multiplex protocol, the MS/MS spectrum may not contain all component intensities required for ratio calculation.

If hasPeptideRatio(const ms_peptide_quant_key&, std::string) const returns false for the given peptide quant key and ratio name, then the peptide ratio object returned by this method represents an undefined ("missing") value.

Using the Average protocol in ms_customquantitation: If quantitation protocol is Average, peptide ratios are interpreted as raw intensity values. It is usually meaningless to define more than one ratio name in this case.

Parameters:
keyThe peptide quant key of the peptide ratio.
ratioNameThe name of the ratio.
Returns:
The peptide ratio. If hasPeptideRatio() returns false, the field values of the object returned by this method are undefined.

Implements ms_quantitation.

double getPeptideRatioNormalisationBase ( const std::string &  ratioName ) const [inherited]

Get the peptide ratio normalisation base of the given ratio name.

Using the Average protocol in ms_customquantitation: If quantitation protocol is Average, peptide ratio normalisation has no meaning. It is strongly recommended to not set normalisation constants.

Parameters:
ratioNamePeptide ratio name.
Returns:
The current peptide ratio normalisation base, or 1 if it hasn't been set.
ms_protein_quant_ratio getProteinRatio ( const std::string &  accession,
int  dbIdx,
const std::string &  ratioName,
const ms_peptide_quant_key_vector includeKeys,
const ms_peptide_quant_key_vector excludeKeys 
) const [virtual]

Given the protein accession, database ID and ratio name, return the protein ratio data, overriding the default inclusion and exclusion of the specified peptide quant keys.

The protein ratio is calculated as described in getProteinRatio(const std::string &, int, const std::string &) const, but the two peptide quant key vectors includeKeys and excludeKeys can be used to override default decisions about globally excluded and outlier peptide ratios. The rules are as follows:

  1. If a peptide quant key is globally excluded with setPeptideRatioExcluded(), then giving the peptide quant key in includeKeys causes the peptide quant key to be included regardless ("undo global exclusion").
  2. If a peptide quant key is given in excludeKeys, then the peptide quant key will be always excluded ("exclude locally").

If the peptide quant key is in both includeKeys and excludeKeys, the latter takes precedence and the peptide quant key is excluded.

Note that if outlier detection is enabled, then a peptide quant key determined to be an outlier cannot be included back using includeKeys, i.e. the inclusion mechanism does not undo outlier removal. You can disable outlier removal entirely before calling getProteinRatio() if you do not want peptide quant keys to be removed.

Using the Average protocol in ms_customquantitation: If quantitation protocol is Average, then the effect of excludeKeys depends on whether the peptide quant key describes a "top N" peptide intensity. If the peptide intensity is one of the top N intensities assigned to this protein, then excluding it means the next highest outside the top N intensities will take its place. No peptide quant keys will ever be excluded automatically as outliers, since outlier removal has no meaning in this protocol.

Parameters:
accessionThe protein accession.
dbIdxThe protein database index.
ratioNameThe name of the ratio.
includeKeysPeptide quant keys to always include, even if they are globally excluded or would be marked as outliers.
excludeKeysPeptide quant keys to always exclude, even if they are not outliers.
Returns:
The protein ratio as calculated from peptide ratios associated with this protein accession. If the ratio could not be calculated (e.g. there are no associated peptide ratios), then the returned object will represent an undefined ("missing") value.

Implements ms_quantitation.

ms_protein_quant_ratio getProteinRatio ( const std::string &  accession,
int  dbIdx,
const std::string &  ratioName 
) const [virtual]

Given the protein accession, database ID and ratio name, return the protein ratio data.

Protein ratios are calculated on demand from the current protein-peptide mapping using the current quantitation method and taking peptide exclusion into account. You can exclude peptides from protein ratio calculation by using setPeptideRatioExcluded(). The current outlier detection method may also change which peptide ratios are used for any given protein.

For ms_ms2quantitation, the protein-peptide mapping is immutable. There are three types of protein ratio, which can be changed with setProteinRatioType(): median, average and weighted. Median is the median of all peptide ratios associated with the protein hit, and average is the geometric mean (equivalently, the arithmetic mean of log-transformed peptide ratios). Weighted is a weighted mean of peptide ratios, where the weights are channel intensities. The weighted ratio type is only available for Reporter data.

For ms_customquantitation, you can change the protein-peptide mapping by associating different peptide quant keys with the protein accession; see ms_customquantitation::addPeptideQuantKey() for details. There are three types of protein ratio: median, average and weighted. Median and average are the same as in ms_ms2quantitation, except in the Average protocol (see below). Weighted is the weighted geometric mean, where the weighting factor of each peptide ratio must be specified when the peptide ratio is added to the class. This is not the same weighting as in ms_ms2quantitation.

ms1, ms2 and custom protein ratios are calculated using:

It is possible for the protein ratio to be undefined ("missing") even when it has associated peptide ratios, if there are not enough peptide ratios (setMinNumPeptides()), if all of them are marked excluded, or if too many of them are infinite.

If quantitation protocol is Reporter, Multiplex, Replicate or Precursor, the returned protein ratio object contains two p-values: the normality test value and the null hypothesis value.

The log-transformed peptide ratios are assumed normally distributed, and this hypothesis is tested using the Shapiro-Wilk W test. The normality p-value is -1 when the test could not be run (e.g. too few peptide ratios) and otherwise a positive number between 0 and 1. In the latter case, a value of less than 0.05 (or similar threshold) is usually taken as evidence that the log-transformed peptide ratios are not normally distributed, or equivalently that the peptide ratios are not log-normally distributed.

If outlier removal is configured, then outliers will be removed before normality testing. If this makes the normality p-value fall below 0.05, then the outliers will be restored. In this case the original sample was likely not normal to start with, and the normality p-value is calculated based on the original sample. If outlier removal is successful, then the normality p-value is based on the sample from which outliers have been removed, and it always exceeds 0.05.

The second p-value is for the null hypothesis. The null hypothesis is that the protein ratio equals 1.0 (component intensities have equal values). The p-value is -1 if there is only one peptide ratio, and otherwise a positive number between 0 and 1. The test is conducted after outlier removal, if any.

Note that the hypothesis test is done regardless of the p-value of the normality test. This means that you need to decide first if you accept peptide ratio normality before deciding whether to reject or not reject the null hypothesis. If normality is violated, then the hypothesis p-value is meaningless.

You can inspect which peptide quant keys were used in protein ratio calculation and which were ignored, due to being excluded or being outliers, with ms_protein_quant_ratio::getActiveKeys(), ms_protein_quant_ratio::getExcludedKeys() and ms_protein_quant_ratio::getOutlierKeys(). You can "move" peptide quant keys between the last two categories and the first by using the method getProteinRatio(const std::string &, int, const std::string &, const ms_peptide_quant_key_vector &, const ms_peptide_quant_key_vector &) const.

Note about weighted protein ratios: Parser 2.5 and 2.6 do not calculate the standard deviation, standard error or p-values when protein ratio type is weighted in Reporter data. The values are set to -1 ("unavailable"); see ms_protein_quant_ratio::getStandardDeviation(). The values are available in ms_customquantitation, which uses a different weighting formula.

Using the Average protocol in ms_customquantitation: If quantitation protocol is Average, the only supported protein ratio type is "average", which does not mean a geometric average. Rather, the protein ratio is the sum of the "top N" peptide intensities, divided by the sum of the top N peptide intensities of the reference protein (see ms_customquantitation::setAverageReferenceProtein()). Neither outlier removal nor normalisation have any meaning in this protocol, which means no significance tests are done and the returned protein ratio object will not contain any p-values.

For more details on configuring other aspects of protein ratio calculation, please consult the quantitation help pages.

Parameters:
accessionThe protein accession.
dbIdxThe protein database index.
ratioNameThe name of the ratio.
Returns:
The protein ratio as calculated from peptide ratios associated with this protein accession. If the ratio could not be calculated (e.g. there are no associated peptide ratios), then the returned object will represent an undefined ("missing") value.

Implements ms_quantitation.

void getProteinRatioSample ( const std::string &  accession,
int  dbIdx,
const std::string &  ratioName,
const std::vector< ms_peptide_quant_key > &  includeKeys,
const std::vector< ms_peptide_quant_key > &  excludeKeys,
std::vector< double > &  sample,
std::vector< double > &  logSample,
std::vector< double > &  weights,
std::vector< ms_peptide_quant_key > &  activeKeys,
std::map< ms_peptide_quant_key, int > &  inactiveKeys,
double &  normalityPvalue 
) const [protected, inherited]

Find the peptide quant keys associated with the protein, collect their unique peptide ratios, remove outliers (if desired) and return the values as the sample of peptide ratios.

This method uses getSortedFinitePeptideRatioValues() internally to collect the vector of peptide ratios. If there are no peptide quant keys associated with the protein, or if no peptide ratios are associated with with those peptide quant keys, then sample, logSample, activeKeys and inactiveKeys will be empty and normalityPvalue will have an undefined value.

Parameters:
accessionProtein accession.
dbIdxProtein database index.
ratioNameName of the ratio.
includeKeysPrevent these peptide quant keys from being excluded.
excludeKeysPrevent these peptide quant keys from being included.
samplePeptide ratios associated with ratioName and the protein's peptide quant keys, in numerically increasing order.
logSampleLog transform of sample.
weightsWeighting factors corresponding to the order of sample (and logSample).
activeKeysPeptide quant keys corresponding to the order of sample (and logSample).
inactiveKeysPeptide quant keys marked as skipped, excluded or outlier.
normalityPvalueThe p-value that the sample appears to be normally distributed after outlier removal. If less than 0.05, no outliers will have been removed.
const ms_quant_method & getQuantitationMethod (  ) const [inherited]

Return the current quantitation method.

The current (or effective) quantitation method is the original quantitation method given as argument to the constructor (or loaded from the Mascot results file), with possible later modifications, such as changing normalisation or outlier settings.

For ms_ms2quantitation, you cannot change the protocol settings, component definitions or peptide quality settings. You must create a new object with the new settings instead. You are free to change how protein ratios are calculated and set new normalisation parameters. These changes will be reflected in this method's output value.

For ms_customquantitation, same restrictions apply, although it makes little difference, as the class does not use any protocol settings, component definitions or peptide quality settings.

Returns:
The current quantitation method.
const ms_quant_ratio * getReportRatioFromFile ( unsigned int  fileNum,
const std::string &  ratioName 
) const

Return a quantitation ratio matching the given name in the given file.

Parameters:
fileNumInteger between 1 and ms_mascotresfile::getNumberOfResfiles().
ratioNameThe name of the report ratio. This must match exactly (case sensitively) the desired report ratio name.
Returns:
If no such report ratio exists, this method returns NULL. Otherwise the corresponding object is returned.
std::vector< std::string > getReportRatioNamesInFile ( unsigned int  fileNum ) const

Return a list of current report ratio names in the given file.

This method simply returns the names of the report ratios as defined in that file. This is the same order they are defined in the file's embedded quantitation method, unless the report ratios have been later changed with setReportRatioInFile() or setCombinedReportRatio().

Parameters:
fileNumInteger between 1 and ms_mascotresfile::getNumberOfResfiles().
Returns:
The list of report ratio names in file fileNum.
void getSortedFinitePeptideRatioValues ( const std::string &  ratioName,
const std::set< ms_peptide_quant_key > &  keys,
const std::set< ms_peptide_quant_key > &  includeKeys,
const std::set< ms_peptide_quant_key > &  excludeKeys,
std::vector< double > &  values,
std::vector< double > &  weights,
std::vector< ms_peptide_quant_key > &  activeKeys,
std::map< ms_peptide_quant_key, int > &  inactiveKeys 
) const [protected, virtual]

Given a list of q,p values and ratio name, find the non-infinite peptide ratio values and return them in numerically increasing order.

The method looks up all peptide ratios associated with keys (ignoring duplicates) and returns them in numerically increasing order in values. Infinite and missing ratios are ignored. The vector activeKeys contains active peptide quant keys in the same order as values, and the map inactiveKeys contains peptide quant keys associated with the protein ratio but for indicated reasons not included in ratio calculation.

Parameters:
ratioNameThe name of the peptide ratio.
keysA list of (sorted or unsorted) peptide quant keys for which to look up the ratios.
includeKeysPrevent these peptide quant keys from being excluded.
excludeKeysPrevent these peptide quant keys from being included.
valuesPeptide ratios associated with ratioName and the given peptide quant keys.
weightsWeighting factors of corresponding to the order of values.
activeKeysPeptide quant keys corresponding to the order of values.
inactiveKeysPeptide quant keys skipped or excluded.

Implements ms_quantitation.

bool hasIntensityNormalisation (  ) const

Return true if intensity normalisation is enabled and configured.

You can enable and disable component intensity normalisation with setQuantNormalisation(). Note that only the "sum" normalisation is supported and only with the Reporter protocol.

If intensity normalisation is enabled, peptide ratio normalisation will be disabled, and vice versa.

Returns:
True if normalisation is enabled and configured, false otherwise.
bool hasPeptideRatio ( const ms_peptide_quant_key key,
const std::string &  ratioName 
) const [virtual]

Existence check: return true if a peptide ratio with the associated peptide quant key and ratio name exists.

Often, most peptide matches in a Mascot results file have no ratio data. For example, the peptide match could be non-significant or not quantitable (quality check fails); or with Reporter or Multiplex protocol, the MS/MS spectrum may not contain all component intensities required for ratio calculation.

Using the Average protocol in ms_customquantitation: If quantitation protocol is Average, peptide ratios are interpreted as raw intensity values. It is usually meaningless to define more than one ratio name in this case.

Parameters:
keyThe peptide quant key of the peptide ratio.
ratioNameThe name of the ratio.
Returns:
True if the peptide ratio exists; false otherwise.

Implements ms_quantitation.

bool hasPeptideRatioNormalisation (  ) const

Return true if peptide ratio normalisation is enabled and configured.

You can enable and disable peptide ratio normalisation with setQuantNormalisation().

If intensity normalisation is enabled, peptide ratio normalisation will be disabled, and vice versa.

Returns:
True if normalisation is enabled and configured, false otherwise.
bool isPeptideRatioExcluded ( const ms_peptide_quant_key key,
const std::string &  ratioName 
) const [virtual]

Boolean flag: is the given peptide ratio globally excluded from protein ratio calculation?

(This method is redundant; you could also look up the peptide ratio and use ms_peptide_quant_ratio::isExcluded().)

Parameters:
keyThe peptide quant key of the peptide ratio.
ratioNameThe name of the ratio.
Returns:
True if the peptide ratio should be excluded from protein ratio calculation; false otherwise.

Implements ms_quantitation.

bool isValid (  ) const [inherited]

Call this function to determine if there have been any errors.

This will return true unless there have been any fatal errors.

See Error Handling.

Returns:
True is no fatal error occured
See also:
getLastError(), getLastErrorString(), clearAllErrors(), getErrorHandler()
Examples:
common_error.cpp, config_enzymes.cpp, config_fragrules.cpp, config_license.cpp, config_mascotdat.cpp, config_masses.cpp, config_modfile.cpp, config_procs.cpp, config_quantitation.cpp, config_taxonomy.cpp, http_helper_getstring.cpp, peptide_list.cpp, resfile_summary.cpp, and tools_aahelper.cpp.
void normaliseIntensities (  )

Normalise component intensities, or do nothing if intensity normalisation is disabled.

Component intensity normalisation will require loading query data for most or all queries in the file, which can be a time-consuming process. This is why normalisation is not performed automatically once the constructor finishes.

Note that if hasIntensityNormalisation() returns false, then this method does nothing.

void normalisePeptideRatios (  )

Normalise peptide ratios, or do nothing if normalisation is disabled.

Normalisation may require calculating all peptide ratios for all quantifiable peptide matches in the file, which can be a time-consuming process. This is why normalisation is not performed automatically once the constructor finishes. Automatic normalisation is also skipped when you change quantitation method parameters or report ratios, for the same reason.

Note that if hasPeptideRatioNormalisation() returns false, then this method does nothing.

void removeCombinedReportRatio ( const std::string &  ratioName )

Remove the combined quantitation ratio matching the given name from all files.

The report ratio with name ratioName will be removed from all files where it is found. Other files remain unchanged.

Removing a combined report ratio does not alter normalisation constants, because the report ratio is removed from all files simultaneously (and because report ratios are independent of each other with respect to normalisation).

Parameters:
ratioNameThe name of the ratio to remove. If this is the empty string, nothing will be removed.
void removeIntensityNormalisationBase ( const std::string &  componentName )

Reset the intensity normalisation base of the given ratio name.

Resetting means the component intensity normalisation constant is set to 1.0. This has the same effect as calling setIntensityNormalisationBase() with b = 1.

Resetting a normalisation constant is possible even if normalisation settings have been configured with setQuantNormalisation() and normaliseIntensities() has been called. It is generally not a good idea to reset normalisation bases, because it will lead to inconsistent peptide ratios.

Parameters:
componentNameComponent name whose normalisation base is to be reset.
void removeIntensityNormalisationBases (  )

Reset all Intensity normalisation bases.

Resetting all intensity normalisation bases means all component intensities become unnormalised.

Resetting a normalisation constant is possible even if normalisation settings have been configured with setQuantNormalisation() and normaliseIntensities() has been called. It is generally not a good idea to reset normalisation bases, because it will lead to inconsistent peptide ratios.

void removePeptideRatioNormalisationBase ( const std::string &  ratioName ) [inherited]

Reset the peptide ratio normalisation base of the given ratio name.

Resetting means the report ratio normalisation constant is set to 1.0. This has the same effect as calling setPeptideRatioNormalisationBase() with b = 1.

In ms_ms2quantitation, resetting a normalisation constant is possible even if normalisation settings have been configured with setQuantNormalisation() and normalisePeptideRatios() has been called. It is generally not a good idea to reset normalisation bases, because it will lead to inconsistent peptide ratios.

Parameters:
ratioNameRatio name whose normalisation base is to be reset.
void removePeptideRatioNormalisationBases (  ) [inherited]

Reset all peptide ratio normalisation bases.

Resetting all report ratio normalisation bases means all peptide and protein ratios become unnormalised.

In ms_ms2quantitation, resetting a normalisation constant is possible even if normalisation settings have been configured with setQuantNormalisation() and normalisePeptideRatios() has been called. It is generally not a good idea to reset normalisation bases, because it will lead to inconsistent peptide ratios.

void removeReportRatioInFile ( unsigned int  fileNum,
const std::string &  ratioName 
)

Remove the quantitation ratio matching the given name from the given file.

The report ratio with name ratioName will be removed from file fileNum, if it exists. Otherwise nothing is removed.

Removing a report ratio from one file resets its normalisation constant across the whole combined file. You will need to use normalisePeptideRatios() to (re)calculate it. If you are changing multiple report ratios at the same time, it is best to wait until all changes are done before calling normalisePeptideRatios(), as that way you only need to normalise once.

Parameters:
fileNumInteger between 1 and ms_mascotresfile::getNumberOfResfiles().
ratioNameThe name of the ratio to remove. If this is the empty string, nothing will be removed.
void setCombinedReportRatio ( const std::string &  ratioName,
const ms_quant_ratio ratioDef 
)

Add or modify the combined quantitation ratio matching the given name in all files.

This method has does two things, in order:

  1. The report ratio with name ratioName is modified to match ratioDef in all files where it is found.
  2. A new report ratio will be added to files which don't have a report ratio with name ratioName.

Afterwards, all files will have a report ratio definition matching ratioDef, which will be merged in one "column" (since its name is the same in all files).

Note that the name defined in ratioDef can differ from ratioName. There are two use cases:

  1. Adding a new definition: set ratioName to the name of a report ratio that does not yet exist and ratioDef to the definition itself.
    • The name set in ratioDef is ignored.
  2. Updating, replacing and renaming a definition: set ratioName to the name of an existing report ratio and pass in ratioDef.
    • If ratioDef name is empty or equals ratioName, then the existing definition will be updated.
    • If ratioDef name differs from ratioName, then the existing definition will be replaced with ratioDef. (If the body of ratioDef is the same as before, this is a rename and otherwise a replace operation.)

Note that if ratioName is the empty string, this method does nothing and returns immediately.

Changing a combined report ratio resets all normalisation constants -- that is, peptide ratios become unnormalised. Use normalisePeptideRatios() to recalculate the normalisation constants.

Parameters:
ratioNameThe name of the ratio to replace, or the name of the new ratio to add. If this is the empty string, a new report ratio will be added.
ratioDefThe ratio definition.
void setIntensityNormalisationBase ( const std::string &  componentName,
double  b 
)

Set the intensity normalisation base of the given component name.

Setting component intensity normalisation to a particular value means all peptide ratios calculated from componentName will be affected. However, the underlying compnent intensities remain unaffected, which means this method will always return immediately without computing anything.

It is not a good idea to define both peptide ratio normalisation and component intensity normalisation at the same time. In fact, you can only configure one or the other using setQuantNormalisation(), and neither normalisePeptideRatios() nor normaliseIntensities() will step on each other's toes.

It is possible, but not recommended, to manually set normalisation bases for both peptide ratios and component intensities. The resulting peptide ratios are most likely meaningless.

You can always set b to 1 to disable component intensity componentName normalisation.

Parameters:
componentNameComponent name to normalise.
bNew normalisation base. If it is zero, the old base will be kept. If this is the first time the base is set, a value of 0 means it is set to 1.0.
void setMinNumPeptides ( int  value ) [inherited]

Set the minimum number of peptides needed for protein ratio calculation.

Changing the minimum number of peptides changes the current quantitation method. It does not alter the original quantitation method object.

Using the Average protocol in ms_customquantitation: The Average protocol has two settings for minimum number of peptides. This setting defines how many peptide intensities are needed for a protein before its ratio can be calculated. It is usually meaningless to choose a value other than 1. Use ms_customquantitation::setAverageNumPeptides() to define how many intensities should be used in protein ratio calculation.

Parameters:
valueThe minimum number of peptide ratios (the sample size) a protein must have for protein ratio calculation purposes. Values less than 1 are interpreted as 1.
void setPeptideRatioExcluded ( const ms_peptide_quant_key key,
const std::string &  ratioName 
) [virtual]

Globally exclude a particular peptide ratio from protein ratio calculation.

All peptide matches associated with a protein ratio are used in calculating that protein's ratio, assuming the peptide ratio passes outlier testing (if used). This may not be desirable in some cases; for example, visual inspection could indicate the peptide match is incorrect. You can use setPeptideRatioExcluded() and setPeptideRatioIncluded() to globally exclude or include individual peptide ratios.

Parameters:
keyThe peptide quant key of the peptide ratio.
ratioNameThe name of the ratio.

Implements ms_quantitation.

void setPeptideRatioIncluded ( const ms_peptide_quant_key key,
const std::string &  ratioName 
) [virtual]

Globally include a particular peptide ratio in protein ratio calculation.

All peptide matches associated with a protein ratio are used in calculating that protein's ratio, assuming the peptide ratio passes outlier testing (if used). This may not be desirable in some cases; for example, visual inspection could indicate the peptide match is incorrect. You can use setPeptideRatioExcluded() and setPeptideRatioIncluded() to globally exclude or include individual peptide ratios.

Parameters:
keyThe peptide quant key of the peptide ratio.
ratioNameThe name of the ratio.

Implements ms_quantitation.

void setPeptideRatioNormalisationBase ( const std::string &  ratioName,
double  b 
) [inherited]

Set the peptide ratio normalisation base of the given ratio name.

Setting peptide ratio normalisation to a particular value means all peptide ratios with ratioName will be divided by b before they are returned by getPeptideRatio(). That is, the underlying peptide ratios remain unaffected, which means this method will always return immediately without computing anything.

In ms_ms2quantitation, normalisation constants can most easily be calculated with ms_ms2quantitation::normalisePeptideRatios(), if normalisation is enabled and configured in the quantitation method. You are free to override this, but keeping track of who calculated which constant is up to you.

It is not a good idea to define both peptide ratio normalisation and component intensity normalisation at the same time. In fact, you can only configure one or the other using setQuantNormalisation(), and neither normalisePeptideRatios() nor normaliseIntensities() will step on each other's toes.

It is possible, but not recommended, to manually set normalisation bases for both peptide ratios and component intensities. The resulting peptide ratios are most likely meaningless.

In ms_customquantitation, you can use ms_customquantitation::getUnnormalisedAveragePeptideRatio() to calculate the mean or median of peptide ratios currently stored in the class, for normalisation purposes.

You can always set b to 1 to disable peptide ratio ratioName normalisation.

Using the Average protocol in ms_customquantitation: If quantitation protocol is Average, peptide ratio normalisation has no meaning. It is strongly recommended to not set normalisation constants.

Parameters:
ratioNamePeptide ratio name to normalise.
bNew normalisation base. If it is zero, the old base will be kept. If this is the first time the base is set, a value of 0 means it is set to 1.0.
void setProteinRatioType ( const char *  value ) [virtual]

Set the protein ratio type.

Changing the protein ratio type changes the current quantitation method. It does not alter the original quantitation method object.

ms_ms2quantitation supports "median", "average" and "weighted", and ms_customquantitation supports "median" and "average. If the ratio type is not implemented, it is set to "median".

Using the Average protocol in ms_customquantitation: If quantitation protocol is Average, the only supported protein ratio type is "average". Setting it to anything else will result in an error. You should inspect isValid() and use clearAllErrors() should you accidentally do so.

Parameters:
valueProtein ratio type (e.g. median, average, weighted). Accepted values are defined in the quantitation XML schema.

Implements ms_quantitation.

void setQuantNormalisation ( const ms_quant_normalisation norm )

Set new peptide and protein ratio normalisation settings.

Peptide and protein ratios can be normalised in several ways. Please consult the quantitation configuration help page for details. Changing ratio normalisation settings may involve a delay as the normalisation base is computed from ratio data.

Changing normalisation settings changes the current quantitation method. It does not alter the original quantitation method object.

Changing the settings resets all normalisation constants -- that is, peptide ratios become unnormalised. Use normalisePeptideRatios() to recalculate the normalisation constants.

Parameters:
normA normalisation configuration object. If this is NULL, normalisation will be disabled (equivalent to "none").
void setQuantOutliers ( const ms_quant_outliers qo ) [virtual]

Set new peptide ratio outlier settings.

Peptide ratio outlier detection can be configured in several ways. Please consult the quantitation configuration help page for details.

Changing outlier settings changes the current quantitation method. It does not alter the original quantitation method object.

Using the Average protocol in ms_customquantitation: It is an error to define outlier removal if quantitation protocol is Average. You will need to inspect isValid() and clear the error with clearAllErrors() should you accidentally do so.

Parameters:
qoAn outlier configuration object. If this is NULL, outlier detection will be disabled (equivalent to "none").

Implements ms_quantitation.

void setReportRatioInFile ( unsigned int  fileNum,
const std::string &  ratioName,
const ms_quant_ratio ratioDef 
)

Add or modify the quantitation ratio matching the given name in the given file.

This method does two things, in order:

  1. The report ratio with name ratioName in file fileNum is modified to match ratioDef, if it exists.
  2. Otherwise a new report ratio will be added to file fileNum.

The new report ratio will be merged with report ratios from other files if its name matches any other report ratio's name.

Note that the name defined in ratioDef can differ from ratioName. There are two use cases:

  1. Adding a new definition: set ratioName to the name of a report ratio that does not yet exist in this file and ratioDef to the definition itself.
    • The name set in ratioDef is ignored.
  2. Updating, replacing and renaming a definition: set ratioName to the name of an existing report ratio and pass in ratioDef.
    • If ratioDef name is empty or equals ratioName, then the existing definition will be updated.
    • If ratioDef name differs from ratioName, then the existing definition will be replaced with ratioDef. (If the body of ratioDef is the same as before, this is a rename and otherwise a replace operation.)

Note that if ratioName is the empty string, this method does nothing and returns immediately.

Changing a report ratio resets its normalisation constant across the whole combined file, while a fresh report ratio starts out with a constant of 1.0. You will need to use normalisePeptideRatios() to (re)calculate it. If you are changing multiple report ratios at the same time, it is best to wait until all changes are done before calling normalisePeptideRatios(), as that way you only need to normalise once.

Parameters:
fileNumInteger between 1 and ms_mascotresfile::getNumberOfResfiles().
ratioNameThe name of the ratio to replace, or the name of the new ratio to add. If this is the empty string, a new report ratio will be added.
ratioDefThe ratio definition.

The documentation for this class was generated from the following files:
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:53