#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 |
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factor used to estimate the width of a peak based on generic spacing
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sigma value used for peak finding
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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
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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
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markers nodes in segments with poor correlation (possibly noisy) are rematched using the filtered zone projection
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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.
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