Commit 9e56b195 authored by Renne Thomas's avatar Renne Thomas
Browse files

replace qvalue by FDR

parent c02d2295
......@@ -38,7 +38,7 @@ AutomaticFilterParameters::AutomaticFilterParameters(
other._filter_is_cross_sample_peptide_number;
m_filter_peptide_observed_in_less_samples_than =
other.m_filter_peptide_observed_in_less_samples_than;
m_filterQvalue = other.m_filterQvalue;
m_filterFDR = other.m_filterFDR;
}
AutomaticFilterParameters::~AutomaticFilterParameters()
......@@ -46,9 +46,9 @@ AutomaticFilterParameters::~AutomaticFilterParameters()
}
void
AutomaticFilterParameters::setFilterPeptideQvalue(double qvalue)
AutomaticFilterParameters::setFilterPeptideFDR(double fdr)
{
m_filterQvalue = qvalue;
m_filterFDR = fdr;
}
void
AutomaticFilterParameters::setFilterPeptideEvalue(pappso::pappso_double evalue)
......@@ -72,9 +72,9 @@ AutomaticFilterParameters::setFilterCrossSamplePeptideNumber(bool cross)
_filter_is_cross_sample_peptide_number = cross;
}
double
AutomaticFilterParameters::getFilterPeptideQvalue() const
AutomaticFilterParameters::getFilterPeptideFDR() const
{
return (m_filterQvalue);
return (m_filterFDR);
}
pappso::pappso_double
AutomaticFilterParameters::getFilterPeptideEvalue() const
......@@ -111,9 +111,9 @@ AutomaticFilterParameters::getFilterPeptideObservedInLessSamplesThan() const
}
bool
AutomaticFilterParameters::useQvalue() const
AutomaticFilterParameters::useFDR() const
{
if(m_filterQvalue != -1)
if(m_filterFDR != -1)
{
return true;
}
......
......@@ -34,7 +34,7 @@ class AutomaticFilterParameters
void setFilterPeptideEvalue(pappso::pappso_double evalue);
void setFilterPeptideQvalue(double qvalue);
void setFilterPeptideFDR(double fdr);
void setFilterProteinEvalue(pappso::pappso_double evalue);
void setFilterMinimumPeptidePerMatch(unsigned int number);
......@@ -46,17 +46,17 @@ class AutomaticFilterParameters
void setFilterCrossSamplePeptideNumber(bool cross);
pappso::pappso_double getFilterPeptideEvalue() const;
double getFilterPeptideQvalue() const;
double getFilterPeptideFDR() const;
pappso::pappso_double getFilterProteinEvalue() const;
unsigned int getFilterMinimumPeptidePerMatch() const;
bool getFilterCrossSamplePeptideNumber() const;
unsigned int getFilterPeptideObservedInLessSamplesThan() const;
bool useQvalue() const;
bool useFDR() const;
private:
double m_filterQvalue = -1;
double m_filterFDR = -1;
pappso::pappso_double _filter_minimum_peptide_evalue = 1;
pappso::pappso_double _filter_minimum_protein_evalue = 1;
unsigned int _filter_minimum_peptide_per_match = 1;
......
......@@ -275,7 +275,7 @@ IdentificationDataSource::isValid(
const AutomaticFilterParameters &automatic_filter_parameters) const
{
if(automatic_filter_parameters.useQvalue())
if(automatic_filter_parameters.useFDR())
{
QVariant qvalue =
p_peptide_evidence->getParam(PeptideEvidenceParam::pappso_qvalue);
......@@ -288,7 +288,7 @@ IdentificationDataSource::isValid(
.arg(p_peptide_evidence->getPeptideXtpSp().get()->getSequence()));
}
if(qvalue.toDouble() <
automatic_filter_parameters.getFilterPeptideQvalue())
automatic_filter_parameters.getFilterPeptideFDR())
{
return true;
}
......
......@@ -27,6 +27,12 @@
<layout class="QHBoxLayout" name="horizontalLayout_2">
<item>
<widget class="QLabel" name="labelEngineName">
<property name="font">
<font>
<weight>75</weight>
<bold>true</bold>
</font>
</property>
<property name="text">
<string>Engine name</string>
</property>
......@@ -34,6 +40,12 @@
</item>
<item>
<widget class="QLabel" name="labelEngineVersion">
<property name="font">
<font>
<weight>75</weight>
<bold>true</bold>
</font>
</property>
<property name="text">
<string>Engine Version</string>
</property>
......
......@@ -626,7 +626,7 @@ PeptideTableModel::getTitle(std::int8_t column)
return "Evalue";
break;
case(std::int8_t)PeptideListColumn::qvalue:
return "q-value";
return "cumulated FDR";
break;
case(std::int8_t)PeptideListColumn::experimental_mhplus:
return "observed MH+";
......
......@@ -48,7 +48,7 @@
<string/>
</property>
<property name="currentIndex">
<number>0</number>
<number>3</number>
</property>
<widget class="QWidget" name="identifications">
<attribute name="title">
......@@ -300,7 +300,7 @@
<item>
<widget class="QPushButton" name="pushButton">
<property name="text">
<string>compute q-values on PSM</string>
<string>compute cumulated FDR on PSM</string>
</property>
</widget>
</item>
......
......@@ -54,9 +54,12 @@
</widget>
</item>
<item>
<widget class="QRadioButton" name="qvalue_radio_button">
<widget class="QRadioButton" name="fdr_radio_button">
<property name="toolTip">
<string>filter on peptide FDR</string>
</property>
<property name="text">
<string>&amp;q-value</string>
<string>&amp;FDR</string>
</property>
<attribute name="buttonGroup">
<string notr="true">peptide_threshold_button_group</string>
......@@ -97,23 +100,26 @@
<item row="2" column="0">
<widget class="QLabel" name="label_4">
<property name="text">
<string>peptide q-value</string>
<string>peptide FDR</string>
</property>
</widget>
</item>
<item row="2" column="1">
<widget class="QDoubleSpinBox" name="peptide_qvalue_spinbox">
<widget class="QDoubleSpinBox" name="peptide_fdr_spinbox">
<property name="suffix">
<string>%</string>
</property>
<property name="decimals">
<number>5</number>
<number>1</number>
</property>
<property name="maximum">
<double>1.000000000000000</double>
<double>100.000000000000000</double>
</property>
<property name="singleStep">
<double>0.001000000000000</double>
<double>0.100000000000000</double>
</property>
<property name="value">
<double>0.010000000000000</double>
<double>1.000000000000000</double>
</property>
</widget>
</item>
......@@ -347,7 +353,7 @@
</hints>
</connection>
<connection>
<sender>peptide_qvalue_spinbox</sender>
<sender>peptide_fdr_spinbox</sender>
<signal>valueChanged(double)</signal>
<receiver>AutomaticFilterWidget</receiver>
<slot>doValueChanged(double)</slot>
......@@ -379,7 +385,7 @@
</hints>
</connection>
<connection>
<sender>qvalue_radio_button</sender>
<sender>fdr_radio_button</sender>
<signal>clicked()</signal>
<receiver>AutomaticFilterWidget</receiver>
<slot>doSetParameters()</slot>
......
......@@ -62,14 +62,14 @@ AutomaticFilterWidget::setAutomaticFilterParameters(
_emit_changed = false;
ui->evalue_radio_button->setChecked(true);
ui->peptide_qvalue_spinbox->setDisabled(true);
ui->peptide_fdr_spinbox->setDisabled(true);
ui->peptide_evalue_spinbox->setEnabled(true);
if(_parameters.useQvalue())
if(_parameters.useFDR())
{
ui->qvalue_radio_button->setChecked(true);
ui->fdr_radio_button->setChecked(true);
ui->peptide_evalue_spinbox->setDisabled(true);
ui->peptide_qvalue_spinbox->setEnabled(true);
ui->peptide_fdr_spinbox->setEnabled(true);
}
ui->peptide_evalue_spinbox->setValue(_parameters.getFilterPeptideEvalue());
ui->protein_evalue_spinbox->setValue(_parameters.getFilterProteinEvalue());
......@@ -162,16 +162,16 @@ AutomaticFilterWidget::doValueChanged(double value)
void
AutomaticFilterWidget::doSetParameters()
{
if(ui->qvalue_radio_button->isChecked())
if(ui->fdr_radio_button->isChecked())
{
_parameters.setFilterPeptideQvalue(ui->peptide_qvalue_spinbox->value());
_parameters.setFilterPeptideFDR(ui->peptide_fdr_spinbox->value()/100);
ui->peptide_evalue_spinbox->setDisabled(true);
ui->peptide_qvalue_spinbox->setEnabled(true);
ui->peptide_fdr_spinbox->setEnabled(true);
}
else
{
_parameters.setFilterPeptideQvalue(-1);
ui->peptide_qvalue_spinbox->setDisabled(true);
_parameters.setFilterPeptideFDR(-1);
ui->peptide_fdr_spinbox->setDisabled(true);
ui->peptide_evalue_spinbox->setEnabled(true);
}
if(_emit_changed)
......
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