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MRMRTNormalizer Class Reference

The MRMRTNormalizer will find retention time peptides in data. More...

#include <OpenMS/ANALYSIS/OPENSWATH/MRMRTNormalizer.h>

Static Public Member Functions

static int outlier_candidate (std::vector< double > &x, std::vector< double > &y)
 This function computes a candidate outlier peptide by iteratively leaving one peptide out to find the one which results in the maximum R^2 of a first order linear regression of the remaining ones. The datapoints are submitted as two vectors of doubles (x- and y-coordinates). More...
 
static std::vector< std::pair
< double, double > > 
rm_outliers (std::vector< std::pair< double, double > > &pairs, double rsq_limit, double coverage_limit)
 This function removes potential outliers from a set of paired points. Two thresholds need to be defined, first a lower R^2 limit to accept the regression for the RT normalization and second, the lower limit of peptide coverage. The algorithms then selects candidate outlier peptides and applies the Chauvenet's criterion on the assumption that the residuals are normal distributed to determine whether the peptides can be removed. This is done iteratively until both limits are reached. More...
 
static double chauvenet_probability (std::vector< double > &residuals, int pos)
 This function computes Chauvenet's criterion probability for a vector and a value whose position is submitted. More...
 
static bool chauvenet (std::vector< double > &residuals, int pos)
 This function computes Chauvenet's criterion for a vector and a value whose position is submitted. More...
 

Detailed Description

The MRMRTNormalizer will find retention time peptides in data.

This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.

The principle is adapted from Escher et al. Escher, C. et al. (2012), Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics, 12: 1111-1121.

Member Function Documentation

static bool chauvenet ( std::vector< double > &  residuals,
int  pos 
)
static

This function computes Chauvenet's criterion for a vector and a value whose position is submitted.

Returns
TRUE, if Chauvenet's criterion is fullfilled and the outlier can be removed.
static double chauvenet_probability ( std::vector< double > &  residuals,
int  pos 
)
static

This function computes Chauvenet's criterion probability for a vector and a value whose position is submitted.

Returns
Chauvenet's criterion probability
static int outlier_candidate ( std::vector< double > &  x,
std::vector< double > &  y 
)
static

This function computes a candidate outlier peptide by iteratively leaving one peptide out to find the one which results in the maximum R^2 of a first order linear regression of the remaining ones. The datapoints are submitted as two vectors of doubles (x- and y-coordinates).

Returns
The position of the candidate outlier peptide as supplied by the vector is returned.
Exceptions
Exception::UnableToFitis thrown if fitting cannot be performed
static std::vector<std::pair<double, double> > rm_outliers ( std::vector< std::pair< double, double > > &  pairs,
double  rsq_limit,
double  coverage_limit 
)
static

This function removes potential outliers from a set of paired points. Two thresholds need to be defined, first a lower R^2 limit to accept the regression for the RT normalization and second, the lower limit of peptide coverage. The algorithms then selects candidate outlier peptides and applies the Chauvenet's criterion on the assumption that the residuals are normal distributed to determine whether the peptides can be removed. This is done iteratively until both limits are reached.

Returns
A vector of pairs is returned if the R^2 limit was reached without reaching the coverage limit. If the limits are reached, an exception is thrown.
Exceptions
Exception::UnableToFitis thrown if fitting cannot be performed

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5