Contaminants.h File Reference

#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/QC/QCBase.h>
#include <unordered_set>

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Classes
class	Contaminants
	QualityControl metric: flag PSMs whose peptide sequences match a user-supplied contaminants FASTA (e.g. cRAP) after digestion. More...
struct	Contaminants::ContaminantsSummary
	Result bundle returned per compute call. More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::Contaminants::ContaminantsSummary

struct OpenMS::Contaminants::ContaminantsSummary

Result bundle returned per compute call.

All four ratios are unitless and lie in [0, 1] for non-empty denominators; when the corresponding denominator is 0 the ratio evaluates to NaN.

Collaboration diagram for Contaminants::ContaminantsSummary:

Class Members
double	all_contaminants_ratio	#contaminants in all PSMs / #all PSMs.
double	assigned_contaminants_intensity_ratio	Sum of feature intensities of contaminant feature-attached PSMs / sum of feature intensities of all feature-attached PSMs.
double	assigned_contaminants_ratio	#contaminants in feature-attached PSMs / #feature-attached PSMs.
pair< Int64, Int64 >	empty_features	(Number of features without a peptide hit, total number of features).
double	unassigned_contaminants_ratio	#contaminants in unassigned PSMs / #unassigned PSMs.