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checkresult.h File Reference

#include "allheaders.h"
#include "gelinfo.h"
#include "anacutoff.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 calculate the spacing tolerance to determine if a zone is marker-dominated or not

Functions

void checkPeakPositions (FILE *ERROROUT_FILE, FILE *FLAGOUT_FILE, float **PeakPosition, float *Spacing, int Markerinc, struct GelInfo *GelInfo, struct AnaCutoff *AnaCutoff, int *num_interpolated_markers, int *num_interpolated_data, int *con_interpolated_markers, int *con_interpolated_data, int Verbose)
 Check the number and location of interpolated lanes and markers.
void checkMarkers (FILE *ERROROUT_FILE, FILE *FLAGOUT_FILE, PIX *pixGelin, float **PeakPosition, float *NodePosition, int *ZoneID, struct GelInfo *GelInfo, struct AnaCutoff *AnaCutoff, float **MarkerCorrelation, float **MarkerRoughness, int Verbose)
 checks the marker lane for roughness and correlation
void matchSinglePeak (INT32 **ZoneProjection, struct GelInfo *GelInfo, float **PeakPosition, int zoneID, int laneID)
 rematches a single node using the ZoneProjection provided, nodes interpolated based on the changed node will be re-interpolated
int correctMarkers (FILE *FLAGOUT_FILE, INT32 **ZoneProjection, float **PeakPosition, struct GelInfo *GelInfo, struct AnaCutoff *AnaCutoff, float **MarkerCorrelation, int Verbose)
 markers nodes in segments with poor correlation (possibly noisy) are rematched using the filtered zone projection


Detailed Description

header file for checkresult.c, contain functions to check peak positon, marker correlation and roughness and subsequent correction

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

void checkMarkers FILE *  ERROROUT_FILE,
FILE *  FLAGOUT_FILE,
PIX *  pixGelin,
float **  PeakPosition,
float *  NodePosition,
int *  ZoneID,
struct GelInfo GelInfo,
struct AnaCutoff AnaCutoff,
float **  MarkerCorrelation,
float **  MarkerRoughness,
int  Verbose
 

checks the marker lane for roughness and correlation

A row of data lying on a piece-wise linear line that connects all the nodes for a lane is extracted for each marker lane. These are the representation of the middle of the marker lanes, which are divided up into segmens and then tested for roughness and correlation in segments to catch missing markers and lane skipping Any low roughness cases will flag the gel for inspection

Parameters:
ERROROUT_FILE writable file handle to error reporting file
FLAGOUT_FILE writable file handle to data log file
pixGelin pix representation of gel image
PeakPosition holds y position of all nodes
NodePosition holds x position of nodes in each zone
ZoneID holds zone ID of each column
GelInfo holds various gel parameters
AnaCutoff holds various analysis cutoff
MarkerCorrelation 2D array to hold the correlation values between adjacent markers
MarkerRoughness 2D array to hold the marker roughness values
Verbose turn on text output to screen

void checkPeakPositions FILE *  ERROROUT_FILE,
FILE *  FLAGOUT_FILE,
float **  PeakPosition,
float *  Spacing,
int  Markerinc,
struct GelInfo GelInfo,
struct AnaCutoff AnaCutoff,
int *  num_interpolated_markers,
int *  num_interpolated_data,
int *  con_interpolated_markers,
int *  con_interpolated_data,
int  Verbose
 

Check the number and location of interpolated lanes and markers.

If too many or too big a consecutive group is interpolated in any zone, flag for inspection Also check all the peak positions and make sure the distance between lanes are similar to the generic spacing, flag for inspection otherwise

Parameters:
ERROROUT_FILE writable file handle to error reporting file
FLAGOUT_FILE writable file handle to data log file
PeakPosition holds y position of all nodes
Spacing the dominant spacing in all zones
Markerinc boolean if true, we only match markers in marker-dominant zone, match all lanes otherwise
GelInfo holds various gel parameters
AnaCutoff holds various analysis cutoff
num_interpolated_markers array where total number of interpolated markers in each zone is returned
num_interpolated_data array where total number of interpolated data lanes in each zone is returned
con_interpolated_markers array where highest number of consecutive interpolated markers in each zone is returned
con_interpolated_data array where highest number of consecutive interpolated data lanes in each zone is returned
Verbose turn on text output to screen

int correctMarkers FILE *  FLAGOUT_FILE,
INT32 **  ZoneProjection,
float **  PeakPosition,
struct GelInfo GelInfo,
struct AnaCutoff AnaCutoff,
float **  MarkerCorrelation,
int  Verbose
 

markers nodes in segments with poor correlation (possibly noisy) are rematched using the filtered zone projection

Parameters:
FLAGOUT_FILE writable file handle to data log file
ZoneProjection points to 1D y-projection in each of the zone
PeakPosition holds y position of all nodes
GelInfo holds various gel parameters
AnaCutoff holds various analysis cutoff
MarkerCorrelation 2D array of the correlation values between adjacent markers
Verbose turn on text output to screen

void matchSinglePeak INT32 **  ZoneProjection,
struct GelInfo GelInfo,
float **  PeakPosition,
int  zoneID,
int  laneID
 

rematches a single node using the ZoneProjection provided, nodes interpolated based on the changed node will be re-interpolated

note that there is no psize support for single peak matching.

Parameters:
ZoneProjection 1D along lane (x) projection each of the zone
GelInfo holds various gel parameters
PeakPosition holds y position of all nodes, the appropriate nodes will be updated
zoneID ID of zone of node to be rematched
laneID ID of lane of node to be rematched


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