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position.h File Reference

header file for position.c, contains functions for peak matching and curvature calculations and output More...

#include "allheaders.h"
#include "gelinfo.h"

Go to the source code of this file.

Defines

#define SIGMA_CUTOFF   4
 sigma value used for peak finding
#define FWHM_FACTOR   5.0/9.0
 factor used to estimate the width of a peak based on generic spacing
#define TOLERANCEFACTOR   3.0
 factor used to determine the maximum difference between a peak and template in a match
#define MAXCURVATUREFACTOR   1.6
 factor used to determine the maximum allowed curvature of a node

Functions

int findPeakPosition (FILE *FLAGOUT_FILE, float **PeakPosition, INT32 **ZoneProjection, struct GelInfo *GelInfo, float *Spacing, float minpsizefactor, int Markerinc, int Verbose)
 Find peaks in ZoneProjections and match with nodes by closest distance to the template.
void writeCurvature (FILE *FLAGOUT_FILE, float **PeakPosition, float *NodePosition, struct GelInfo *GelInfo)
 calculates curvature of a set of peak position and node position for all lanes and all zones
int correctOutlierPeaks (float **PeakPosition, float *NodePosition, struct GelInfo *GelInfo, int Verbose)
 finds nodes showing high curvature and correct for them by forcing them to be in a straight line with their neighbours in neighbouring zones
void smoothPeaks (float **PeakPosition, struct GelInfo *GelInfo, int Verbose)
 compare each peak with the mean position of all other nodes in the lane and smooth the overall results by applying a 3 lane x 3 zones median filters to these differences
void fillEmpties (float *PeakPosition, struct GelInfo *GelInfo)
 interpolate for any unplaced nodes (peak position == 0)


Detailed Description

header file for position.c, contains functions for peak matching and curvature calculations and output


Define Documentation

#define FWHM_FACTOR   5.0/9.0
 

factor used to estimate the width of a peak based on generic spacing

See also:
specFindPeak()

#define SIGMA_CUTOFF   4
 

sigma value used for peak finding

See also:
specFindPeak()


Function Documentation

int correctOutlierPeaks float **  PeakPosition,
float *  NodePosition,
struct GelInfo GelInfo,
int  Verbose
 

finds nodes showing high curvature and correct for them by forcing them to be in a straight line with their neighbours in neighbouring zones

Parameters:
PeakPosition holds y position of all nodes
NodePosition holds x position of nodes in each zone
GelInfo holds various gel parameters
Verbose turn on text output to screen
Returns:
the number of outlier nodes corrected

void fillEmpties float *  PeakPosition,
struct GelInfo GelInfo
 

interpolate for any unplaced nodes (peak position == 0)

Parameters:
PeakPosition holds y position to nodes for a zone, 0 denotes unmatched nodes, those nodes will be filled by linearly interpolation or extrapolation
GelInfo holds various gel parameters

int findPeakPosition FILE *  FLAGOUT_FILE,
float **  PeakPosition,
INT32 **  ZoneProjection,
struct GelInfo GelInfo,
float *  Spacing,
float  minpsizefactor,
int  Markerinc,
int  Verbose
 

Find peaks in ZoneProjections and match with nodes by closest distance to the template.

unmatch nodes are interpolated, which are marked using negative numbers

Parameters:
FLAGOUT_FILE writable file handle to data log file
PeakPosition holds y position to nodes for all zones, interpolated nodes are denoted by negative position
ZoneProjection points to 1D y-projection in each of the zone
GelInfo holds various gel parameters
Spacing the dominant spacing in all zones
minpsizefactor peaks are rejected if their psize is smaller than this factor times the psize of the nearest peak matched to a marker node
Markerinc if 1, matches only marker lanes in marker-dominated zones
Verbose turn on text output to screen

void smoothPeaks float **  PeakPosition,
struct GelInfo GelInfo,
int  Verbose
 

compare each peak with the mean position of all other nodes in the lane and smooth the overall results by applying a 3 lane x 3 zones median filters to these differences

Parameters:
PeakPosition holds y position to nodes for all zones, interpolated nodes are denoted by negative position
GelInfo holds various gel parameters
Verbose turn on text output to screen

void writeCurvature FILE *  FLAGOUT_FILE,
float **  PeakPosition,
float *  NodePosition,
struct GelInfo GelInfo
 

calculates curvature of a set of peak position and node position for all lanes and all zones

Parameters:
FLAGOUT_FILE writable file handle to data log file
PeakPosition holds y position of all nodes
NodePosition holds x position of nodes in each zone
GelInfo holds various gel parameters


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