From 3862ecde759388bd6e61ca156519ca45493b3f02 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Fri, 9 Nov 2018 10:48:47 +0100
Subject: [PATCH] display separately fdr on psm and on peptides
---
src/core/identificationgroup.cpp | 10 ++++++++++
src/core/identificationgroup.h | 6 ++++++
src/gui/project_view/project_view.ui | 22 ++++++++++++++++++----
src/gui/project_view/projectwindow.cpp | 12 ++++++++++--
src/output/ods/groupingsheet.cpp | 9 +++++++--
5 files changed, 51 insertions(+), 8 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index b1e394a11..13178ddf3 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -442,6 +442,16 @@ IdentificationGroup::getTabName() const
return _ms_run_list[0]->getSampleName();
}
+pappso::pappso_double
+IdentificationGroup::getPsmFdr(ValidationState state) const
+{
+
+ pappso::pappso_double total_peptide = countPeptideEvidence(state);
+ pappso::pappso_double false_peptide = countDecoyPeptideEvidence(state);
+
+ return (false_peptide / total_peptide);
+}
+
pappso::pappso_double
IdentificationGroup::getPeptideMassFdr(ValidationState state) const
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 7ec739ac5..f723d8b7f 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -125,6 +125,12 @@ class IdentificationGroup
pappso::pappso_double
getPeptideMassFdr(ValidationState state = ValidationState::valid) const;
+ /** @brief get False Discovery Rate of psm, peptide spectrum match (unique
+ * PeptideEvidence object)
+ */
+ pappso::pappso_double
+ getPsmFdr(ValidationState state = ValidationState::valid) const;
+
/** @brief validate or invalidate peptides and proteins based automatic
* filters and manual checks
diff --git a/src/gui/project_view/project_view.ui b/src/gui/project_view/project_view.ui
index af88d8cd4..d37feea53 100644
--- a/src/gui/project_view/project_view.ui
+++ b/src/gui/project_view/project_view.ui
@@ -191,7 +191,7 @@
<string>FDR</string>
</property>
<layout class="QGridLayout" name="gridLayout_4">
- <item row="0" column="1">
+ <item row="1" column="1">
<widget class="QLabel" name="peptide_fdr_label">
<property name="toolTip">
<string/>
@@ -201,21 +201,21 @@
</property>
</widget>
</item>
- <item row="1" column="0">
+ <item row="2" column="0">
<widget class="QLabel" name="label_3">
<property name="text">
<string>FDR on proteins</string>
</property>
</widget>
</item>
- <item row="0" column="0">
+ <item row="1" column="0">
<widget class="QLabel" name="label">
<property name="text">
<string>FDR on peptides</string>
</property>
</widget>
</item>
- <item row="1" column="1">
+ <item row="2" column="1">
<widget class="QLabel" name="protein_fdr_label">
<property name="toolTip">
<string/>
@@ -225,6 +225,20 @@
</property>
</widget>
</item>
+ <item row="0" column="1">
+ <widget class="QLabel" name="psm_fdr_label">
+ <property name="text">
+ <string>0 %</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_6">
+ <property name="text">
+ <string>FDR on psm</string>
+ </property>
+ </widget>
+ </item>
</layout>
</widget>
</item>
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 2d8240d6c..6a0aae86b 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -272,19 +272,27 @@ ProjectWindow::computeFdr()
pappso::pappso_double false_prot = 0;
pappso::pappso_double total_peptide = 0;
pappso::pappso_double false_peptide = 0;
+ pappso::pappso_double total_psm = 0;
+ pappso::pappso_double false_psm = 0;
for(IdentificationGroup *identification_group :
_project_sp.get()->getIdentificationGroupList())
{
total_prot += identification_group->countProteinMatch(state);
false_prot += identification_group->countDecoyProteinMatch(state);
- total_peptide += identification_group->countPeptideEvidence(state);
- false_peptide +=
+ total_psm += identification_group->countPeptideEvidence(state);
+ false_psm +=
identification_group->countDecoyPeptideEvidence(state);
+
+ total_peptide += identification_group->countPeptideMassSample(state);
+ false_peptide +=
+ identification_group->countDecoyPeptideMassSample(state);
}
ui->protein_fdr_label->setText(QString("%1 %").arg(
QString::number((false_prot / total_prot) * 100.0, 'f', 2)));
ui->peptide_fdr_label->setText(QString("%1 %").arg(
QString::number((false_peptide / total_peptide) * 100.0, 'f', 2)));
+ ui->psm_fdr_label->setText(QString("%1 %").arg(
+ QString::number((false_psm / total_psm) * 100.0, 'f', 2)));
}
catch(pappso::PappsoException exception_pappso)
{
diff --git a/src/output/ods/groupingsheet.cpp b/src/output/ods/groupingsheet.cpp
index 156bcacd6..cfebe71c9 100644
--- a/src/output/ods/groupingsheet.cpp
+++ b/src/output/ods/groupingsheet.cpp
@@ -75,6 +75,7 @@ GroupingSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
p_ident->countPeptideMassSample(ValidationState::grouped));
_p_writer->writeCellPercentage(p_ident->getProteinFdr(ValidationState::valid));
_p_writer->writeCellPercentage(p_ident->getPeptideMassFdr(ValidationState::valid));
+ _p_writer->writeCellPercentage(p_ident->getPsmFdr(ValidationState::valid));
}
@@ -106,11 +107,15 @@ GroupingSheet::writeHeaders()
"peptide sequence+modifications+sample name");
_p_writer->writeCell("peptide/mass/sample");
_p_writer->setCellAnnotation(
- "FDR at the protein level (number of decoy valid proteins / totale number "
+ "FDR at the protein level (number of decoy valid proteins / total number "
"of valid proteins)");
_p_writer->writeCell("prot FDR");
_p_writer->setCellAnnotation(
- "FDR at the peptide level (number of decoy valid peptides / totale number "
+ "FDR at the peptide level (number of decoy valid peptides / total number "
"of valid peptides)");
_p_writer->writeCell("pep FDR");
+ _p_writer->setCellAnnotation(
+ "FDR at the peptide spectrum match (peptide evidences for each association of a spectrum to a peptide, overall identification engines) level (number of decoy valid psms / total number "
+ "of valid peptides)");
+ _p_writer->writeCell("psm FDR");
}
--
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