From 52d4943c54ef60f693bfc4f14a9e826acc334b73 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Tue, 28 Mar 2017 15:50:39 +0200
Subject: [PATCH] compute corrected Evalue for proteins
---
src/core/proteinmatch.cpp | 42 ++++++++++++++++++++++++++++++++++++++-
src/core/proteinmatch.h | 33 ++++++++++++++++++++----------
2 files changed, 64 insertions(+), 11 deletions(-)
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 9df85654..3a09a982 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -83,7 +83,8 @@ void ProteinMatch::setEvalue(pappso::pappso_double evalue) {
}
pappso::pappso_double ProteinMatch::getEvalue() const {
- return _evalue;
+ pappso::MsRunIdSp sp_msrun_id;
+ return getEvalue(sp_msrun_id);
}
void ProteinMatch::setProteinXtpSp(ProteinXtpSp protein_sp) {
_protein_sp = protein_sp;
@@ -181,6 +182,45 @@ unsigned int ProteinMatch::countValidAndCheckedPeptideMassCharge(const pappso::M
return sequence_list.size();
}
+pappso::pappso_double ProteinMatch::getEvalue(const pappso::MsRunIdSp & sp_msrun_id) const {
+ std::map<QString, pappso::pappso_double> map_sequence_evalue;
+ for (auto & p_peptide_match : _peptide_match_list) {
+ if (p_peptide_match->isValidAndChecked()) {
+ QString sequence(p_peptide_match->getPeptideXtpSp().get()->getSequence());
+ pappso::pappso_double evalue = p_peptide_match->getEvalue();
+ if(sp_msrun_id.get() != nullptr) {
+ //within sample
+ if (p_peptide_match->getMsRunIdSp().get() == sp_msrun_id.get()) {
+ auto ret = map_sequence_evalue.insert(std::pair<QString, pappso::pappso_double>(sequence, evalue));
+ if (ret.second == false) {
+ if (ret.first->second < evalue) {//get best evalue for sequence
+ ret.first->second = evalue;
+ }
+ }
+ }
+ }
+ else {
+ //overall samples
+ auto ret = map_sequence_evalue.insert(std::pair<QString, pappso::pappso_double>(sequence, evalue));
+ if (ret.second == false) {
+ if (ret.first->second < evalue) {//get best evalue for sequence
+ ret.first->second = evalue;
+ }
+ }
+ }
+ }
+ }
+
+ pappso::pappso_double evalue_prot = 1;
+ for (auto && peptide_pair: map_sequence_evalue) {
+ //evalue_prot += std::log10(peptide_pair.second);
+ evalue_prot *= peptide_pair.second;
+ }
+
+ //return (std::pow ((double) 10.0,evalue_prot));
+ return (evalue_prot);
+
+}
pappso::pappso_double ProteinMatch::getPAI() const {
pappso::MsRunIdSp sp_msrun_id;
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index d649e355..9460c4c1 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -37,26 +37,37 @@ class IdentificationGroup;
class ProteinMatch
{
- friend IdentificationGroup;
+ friend IdentificationGroup;
public:
ProteinMatch();
~ProteinMatch();
const ProteinXtpSp & getProteinXtpSp() const;
void setEvalue(pappso::pappso_double evalue);
+
+ /** @brief compute protein Evalue overall samples
+ * */
pappso::pappso_double getEvalue() const;
- pappso::pappso_double getCoverage() const;
- /** @brief compute Protein Abundance Index (PAI)
- * overall sample PAI computation (Rappsilber et al. 2002)
- * */
+ /** @brief compute protein Evalue within samples
+ * */
+ pappso::pappso_double getEvalue(const pappso::MsRunIdSp & sp_msrun_id) const;
+
+
+ /** @brief protein coverage overall samples
+ * */
+ pappso::pappso_double getCoverage() const;
+
+ /** @brief compute Protein Abundance Index (PAI)
+ * overall sample PAI computation (Rappsilber et al. 2002)
+ * */
pappso::pappso_double getPAI() const;
/** @brief compute Protein Abundance Index (PAI) within sample
* PAI computation (Rappsilber et al. 2002)
* */
pappso::pappso_double getPAI(const pappso::MsRunIdSp & sp_msrun_id) const;
-
+
void setProteinXtpSp(ProteinXtpSp protein_sp);
void addPeptideMatch(PeptideMatch * peptide_match);
std::vector<PeptideMatch *> & getPeptideMatchList();
@@ -81,17 +92,20 @@ public:
const pappso::GrpProteinSp & getGrpProteinSp() const;
const GroupingGroupSp & getGroupingGroupSp() const;
-
+
protected :
-
+
/** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
void setGroupingExperiment(GroupingExperiment * p_grp_experiment);
-
+
void setGroupInstance(GroupStore & group_store);
+private :
+ unsigned int countValidAndCheckedPeptideMassCharge(const pappso::MsRunIdSp & sp_msrun_id) const;
+
private:
pappso::GrpProteinSp _sp_grp_protein;
GroupingGroupSp _sp_group;
@@ -106,7 +120,6 @@ private:
/** @brief automatic filter result (false by default)
*/
bool _proxy_valid = false;
- unsigned int countValidAndCheckedPeptideMassCharge(const pappso::MsRunIdSp & sp_msrun_id) const;
};
--
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