Skip to content

Improve slightly procedure for best ploidy detection #50

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
gladkia wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Improve slightly procedure for best ploidy detection #50

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
30f81aa
Improve slightly procedure for best ploidy detection
gladkia Feb 13, 2019
ef2113e
Bump version
gladkia Feb 13, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
25 changes: 24 additions & 1 deletion src/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1009,17 +1009,40 @@ int main(int argc, char *argv[])
int secondBest= ploidies[max_element(percentage_GenExpl.begin(),percentage_GenExpl.end())-percentage_GenExpl.begin()];
cout << "..Best ploidy could have been set to "<<secondBest << " according to the percentage of the copy number changes explained by a model with a given ploidy"<<endl;

/*
So far null ploidy was reset from 4 to 2 if fraction of genome explained in case of
ploidy = 2 was higher, equal or only slightly lower compared to ploidy = 4 case.
In detail, the difference between fractions must have been < 0.05

Here the 'genomeExplainedMaxDiff' config parameter is introduced to let the user decide.
The default value for the param is 0.05
*/
double genomeExplainedMaxDiff = (double)cf.Value("general", "genomeExplainedMaxDiff", 0.05);
cout << "..genomeExplanedMaxDiff set to: "<<genomeExplainedMaxDiff << "."<<endl;

if (bestPloidy==4 && std::find(ploidies.begin(), ploidies.end(), 2) != ploidies.end()) {
int ind2=std::find(ploidies.begin(), ploidies.end(), 2)-ploidies.begin();
int ind4=std::find(ploidies.begin(), ploidies.end(), 4)-ploidies.begin();

if (percentage_GenExpl[ind4]-percentage_GenExpl[ind2]<0.05 || unexplainedChromosomes[ind2]<=1) {
if (percentage_GenExpl[ind4]-percentage_GenExpl[ind2]<genomeExplainedMaxDiff || unexplainedChromosomes[ind2]<=1) {
bestPloidy=2;
cout << "..Changed ploidy to 2 as there is little difference in the fit betweeen ploidies 4 and 2:" << endl;
cout << "unexplained regions for ploidy 2 are located on " <<unexplainedChromosomes[ind2]<< " chromosomes"<< endl;
}
}

// Add also scenario 3 => 2 for best ploidy. Use same rules as in case of 4 => 2 change
if (bestPloidy==3 && std::find(ploidies.begin(), ploidies.end(), 2) != ploidies.end()) {
int ind2=std::find(ploidies.begin(), ploidies.end(), 2)-ploidies.begin();
int ind3=std::find(ploidies.begin(), ploidies.end(), 3)-ploidies.begin();

if (percentage_GenExpl[ind3]-percentage_GenExpl[ind2]<genomeExplainedMaxDiff || unexplainedChromosomes[ind2]<=1) {
bestPloidy=2;
cout << "..Changed ploidy to 2 as there is little difference in the fit betweeen ploidies 3 and 2:" << endl;
cout << "unexplained regions for ploidy 2 are located on " <<unexplainedChromosomes[ind2]<< " chromosomes"<< endl;
}
}



if (bestPloidy!=ploidies.back()) {
Expand Down
2 changes: 1 addition & 1 deletion src/version.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
#define VERSION_H

const double VERSION_OFFSET = 3;
const double FREEC_VERSION = 11.5;
const double FREEC_VERSION = 11.6;
const double CONTROL_FREEC_VERSION = FREEC_VERSION - VERSION_OFFSET;

#endif