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FilteringEditorIllumina.m
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FilteringEditorIllumina.m
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function varargout = FilteringEditorIllumina(varargin)
% FILTERINGEDITORILLUMINA M-file for FilteringEditorIllumina.fig
% FILTERINGEDITORILLUMINA, by itself, creates a new FILTERINGEDITORILLUMINA or raises the existing
% singleton*.
%
% H = FILTERINGEDITORILLUMINA returns the handle to a new FILTERINGEDITORILLUMINA or the handle to
% the existing singleton*.
%
% FILTERINGEDITORILLUMINA('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in FILTERINGEDITORILLUMINA.M with the given input arguments.
%
% FILTERINGEDITORILLUMINA('Property','Value',...) creates a new FILTERINGEDITORILLUMINA or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before FilteringEditorIllumina_OpeningFunction gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to FilteringEditorIllumina_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help FilteringEditorIllumina
% Last Modified by GUIDE v2.5 15-Jun-2012 11:29:09
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @FilteringEditorIllumina_OpeningFcn, ...
'gui_OutputFcn', @FilteringEditorIllumina_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before FilteringEditorIllumina is made visible.
function FilteringEditorIllumina_OpeningFcn(hObject, eventdata, handles, varargin)
% Set Window size and Position
screensize=get(0,'screensize');
winsize=get(handles.FilteringEditorIllumina,'Position');
winwidth=winsize(3);
winheight=winsize(4);
screenwidth=screensize(3);
screenheight=screensize(4);
winpos=[0.5*(screenwidth-winwidth),0.5*(screenheight-winheight),winwidth,winheight];
set(handles.FilteringEditorIllumina,'Position',winpos);
% Get inputs
handles.invertFlag=varargin{1};
if (handles.invertFlag)
set(handles.invertCheck,'Enable','on')
else
set(handles.invertCheck,'Enable','off')
end
% Set defaults
handles.alphalims=[0.98 0.99]; % Limits for MAS5 P, A, or M
handles.margasabs=true; % Marginal as absents
handles.iqr=[]; % IQR below percentile
handles.var=[]; % Variance below percentile
handles.inten=[]; % Intensity cutoff
handles.custom=''; % No custom filter
handles.nofilt=false; % Filtering or not
handles.invert=false; % Invert the detaection score
handles.export=false; % Do not export filtered genes
handles.usewaitbar=true; % Do not use waitbars
handles.outlierTest='none'; % None
handles.pval=[]; % Since test defaults to none
handles.dishis=false; % Do not display histograms
handles.cancel=false; % Cancel not pressed
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes FilteringEditorAffy wait for user response (see UIRESUME)
uiwait(handles.FilteringEditorIllumina);
% --- Outputs from this function are returned to the command line.
function varargout = FilteringEditorIllumina_OutputFcn(hObject, eventdata, handles)
if (get(handles.cancelButton,'Value')==0)
delete(handles.FilteringEditorIllumina);
elseif (get(handles.okButton,'Value')==0)
delete(handles.FilteringEditorIllumina);
end
varargout{1}=handles.alphalims;
varargout{2}=handles.margasabs;
varargout{3}=handles.iqr;
varargout{4}=handles.var;
varargout{5}=handles.inten;
varargout{6}=handles.custom;
varargout{7}=handles.nofilt;
varargout{8}=handles.invert;
varargout{9}=handles.export;
varargout{10}=handles.usewaitbar;
varargout{11}=handles.outlierTest;
varargout{12}=handles.pval;
varargout{13}=handles.dishis;
varargout{14}=handles.cancel;
function pCallCheck_Callback(hObject, eventdata, handles)
if get(hObject,'Value')==1
set(handles.pCallMarginStatic,'Enable','on')
set(handles.pCallLowStatic,'Enable','on')
set(handles.pCallUpStatic,'Enable','on')
set(handles.pCallLowEdit,'Enable','on')
set(handles.pCallUpEdit,'Enable','on')
set(handles.margAsAbsCheck,'Enable','on')
handles.alphalims(1)=str2double(get(handles.pCallLowEdit,'String'));
handles.alphalims(2)=str2double(get(handles.pCallUpEdit,'String'));
else
set(handles.pCallMarginStatic,'Enable','off')
set(handles.pCallLowStatic,'Enable','off')
set(handles.pCallUpStatic,'Enable','off')
set(handles.pCallLowEdit,'Enable','off')
set(handles.pCallUpEdit,'Enable','off')
set(handles.margAsAbsCheck,'Enable','off')
handles.alphalims=[];
end
checkCheck(handles);
guidata(hObject,handles);
% --- Executes on button press in invertCheck.
function invertCheck_Callback(hObject, eventdata, handles)
if get(hObject,'Value')==1
handles.invertScore=1;
else
handles.invertScore=0;
end
guidata(hObject,handles);
function pCallLowEdit_Callback(hObject, eventdata, handles)
p=str2double(get(hObject,'String'));
if isnan(p) || p<0 || p>1
uiwait(errordlg('Lower detection limit must be a number between 0 and 1','Bad Input','modal'));
set(hObject,'String','0.98');
else
handles.alphalims(1)=p;
end
guidata(hObject,handles);
function pCallLowEdit_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function pCallUpEdit_Callback(hObject, eventdata, handles)
p=str2double(get(hObject,'String'));
if isnan(p) || p<0 || p>1
uiwait(errordlg('Upper detection limit must be a number between 0 and 1','Bad Input','modal'));
set(hObject,'String','0.99');
else
handles.alphalims(2)=p;
end
guidata(hObject,handles);
function pCallUpEdit_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function margAsAbsCheck_Callback(hObject, eventdata, handles)
if get(hObject,'Value')==1
handles.margasabs=true;
else
handles.margasabs=false;
end
guidata(hObject,handles);
function iqrCheck_Callback(hObject, eventdata, handles)
if get(hObject,'Value')==1
set(handles.iqrStatic,'Enable','on')
set(handles.iqrEdit,'Enable','on')
handles.iqr=str2double(get(handles.iqrEdit,'String'));
else
set(handles.iqrStatic,'Enable','off')
set(handles.iqrEdit,'Enable','off')
handles.iqr=[];
end
checkCheck(handles);
guidata(hObject,handles);
function varCheck_Callback(hObject, eventdata, handles)
if get(hObject,'Value')==1
set(handles.varStatic,'Enable','on')
set(handles.varEdit,'Enable','on')
handles.var=str2double(get(handles.varEdit,'String'));
else
set(handles.varStatic,'Enable','off')
set(handles.varEdit,'Enable','off')
handles.var=[];
end
checkCheck(handles);
guidata(hObject,handles);
function intenCheck_Callback(hObject, eventdata, handles)
if get(hObject,'Value')==1
set(handles.intenStatic,'Enable','on')
set(handles.intenEdit,'Enable','on')
handles.inten=str2double(get(handles.intenEdit,'String'));
else
set(handles.intenStatic,'Enable','off')
set(handles.intenEdit,'Enable','off')
handles.inten=[];
end
guidata(hObject,handles);
function customCheck_Callback(hObject, eventdata, handles)
if get(hObject,'Value')==1
set(handles.customEdit,'Enable','on')
set(handles.pCallCheck,'Enable','off')
set(handles.pCallMarginStatic,'Enable','off')
set(handles.pCallLowStatic,'Enable','off')
set(handles.pCallUpStatic,'Enable','off')
set(handles.pCallLowEdit,'Enable','off')
set(handles.pCallUpEdit,'Enable','off')
set(handles.margAsAbsCheck,'Enable','off')
set(handles.iqrCheck,'Enable','off')
set(handles.iqrStatic,'Enable','off')
set(handles.iqrEdit,'Enable','off')
set(handles.varCheck,'Enable','off')
set(handles.varStatic,'Enable','off')
set(handles.varEdit,'Enable','off')
set(handles.intenCheck,'Enable','off')
set(handles.intenStatic,'Enable','off')
set(handles.intenEdit,'Enable','off')
handles.alphalims=[];
handles.iqr=[];
handles.var=[];
handles.inten=[];
else
set(handles.customEdit,'Enable','off')
set(handles.pCallCheck,'Enable','on')
set(handles.iqrCheck,'Enable','on')
set(handles.varCheck,'Enable','on')
set(handles.intenCheck,'Enable','on')
if get(handles.pCallCheck,'Value')==1
set(handles.pCallMarginStatic,'Enable','on')
set(handles.pCallLowStatic,'Enable','on')
set(handles.pCallUpStatic,'Enable','on')
set(handles.pCallLowEdit,'Enable','on')
set(handles.pCallUpEdit,'Enable','on')
set(handles.margAsAbsCheck,'Enable','on')
handles.alphalims(1)=str2double(get(handles.pCallLowEdit,'String'));
handles.alphalims(2)=str2double(get(handles.pCallUpEdit,'String'));
end
if get(handles.iqrCheck,'Value')==1
set(handles.iqrStatic,'Enable','on')
set(handles.iqrEdit,'Enable','on')
handles.iqr=str2double(get(handles.iqrEdit,'String'));
end
if get(handles.varCheck,'Value')==1
set(handles.varStatic,'Enable','on')
set(handles.varEdit,'Enable','on')
handles.var=str2double(get(handles.varEdit,'String'));
end
if get(handles.intenCheck,'Value')==1
set(handles.intenStatic,'Enable','on')
set(handles.intenEdit,'Enable','on')
handles.inten=str2double(get(handles.intenEdit,'String'));
end
end
guidata(hObject,handles);
function nofiltCheck_Callback(hObject, eventdata, handles)
if get(hObject,'Value')==1
set(handles.pCallCheck,'Enable','off')
set(handles.pCallMarginStatic,'Enable','off')
set(handles.pCallLowStatic,'Enable','off')
set(handles.pCallUpStatic,'Enable','off')
set(handles.pCallLowEdit,'Enable','off')
set(handles.pCallUpEdit,'Enable','off')
set(handles.margAsAbsCheck,'Enable','off')
set(handles.invertCheck,'Enable','off')
set(handles.iqrCheck,'Enable','off')
set(handles.iqrStatic,'Enable','off')
set(handles.iqrEdit,'Enable','off')
set(handles.varCheck,'Enable','off')
set(handles.varStatic,'Enable','off')
set(handles.varEdit,'Enable','off')
set(handles.intenCheck,'Enable','off')
set(handles.intenStatic,'Enable','off')
set(handles.intenEdit,'Enable','off')
set(handles.customCheck,'Enable','off')
set(handles.customEdit,'Enable','off')
set(handles.outlierPopup,'Enable','off')
set(handles.pcutStatic,'Enable','off')
set(handles.pcutEdit,'Enable','off')
set(handles.disphistCheck,'Enable','off')
handles.nofilt=true;
handles.alphalims=[];
handles.iqr=[];
handles.var=[];
handles.inten=[];
handles.custom='';
else
set(handles.pCallCheck,'Enable','on')
set(handles.iqrCheck,'Enable','on')
set(handles.varCheck,'Enable','on')
set(handles.intenCheck,'Enable','on')
set(handles.customCheck,'Enable','on')
if get(handles.pCallCheck,'Value')==1
set(handles.pCallAlphaStatic,'Enable','on')
set(handles.pCallLowStatic,'Enable','on')
set(handles.pCallUpStatic,'Enable','on')
set(handles.pCallLowEdit,'Enable','on')
set(handles.pCallUpEdit,'Enable','on')
set(handles.margAsAbsCheck,'Enable','on')
handles.alphalims(1)=str2double(get(handles.pCallLowEdit,'String'));
handles.alphalims(2)=str2double(get(handles.pCallUpEdit,'String'));
end
if get(handles.iqrCheck,'Value')==1
set(handles.iqrStatic,'Enable','on')
set(handles.iqrEdit,'Enable','on')
handles.iqr=str2double(get(handles.iqrEdit,'String'));
end
if get(handles.varCheck,'Value')==1
set(handles.varStatic,'Enable','on')
set(handles.varEdit,'Enable','on')
handles.var=str2double(get(handles.varEdit,'String'));
end
if get(handles.intenCheck,'Value')==1
set(handles.intenStatic,'Enable','on')
set(handles.intenEdit,'Enable','on')
handles.inten=str2double(get(handles.intenEdit,'String'));
end
if get(handles.customCheck,'Value')==1
set(handles.customEdit,'Enable','on')
handles.custom=get(handles.customEdit,'String');
end
set(handles.outlierPopup,'Enable','on')
if get(handles.outlierPopup,'Value')==1
set(handles.pcutStatic,'Enable','off')
set(handles.pcutEdit,'Enable','off')
set(handles.disphistCheck,'Enable','off')
else
set(handles.pcutStatic,'Enable','on')
set(handles.pcutEdit,'Enable','on')
set(handles.disphistCheck,'Enable','on')
end
handles.nofilt=false;
end
guidata(hObject,handles);
function iqrEdit_Callback(hObject, eventdata, handles)
function iqrEdit_CreateFcn(hObject, eventdata, handles)
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function varEdit_Callback(hObject, eventdata, handles)
function varEdit_CreateFcn(hObject, eventdata, handles)
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function intenEdit_Callback(hObject, eventdata, handles)
function intenEdit_CreateFcn(hObject, eventdata, handles)
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function customEdit_Callback(hObject, eventdata, handles)
function customEdit_CreateFcn(hObject, eventdata, handles)
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function exportFiltCheck_Callback(hObject, eventdata, handles)
function useWaitCheck_Callback(hObject, eventdata, handles)
function outlierPopup_Callback(hObject, eventdata, handles)
function outlierPopup_CreateFcn(hObject, eventdata, handles)
% Hint: popupmenu controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function pcutEdit_Callback(hObject, eventdata, handles)
function pcutEdit_CreateFcn(hObject, eventdata, handles)
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function disphistCheck_Callback(hObject, eventdata, handles)
function okButton_Callback(hObject, eventdata, handles)
uiresume(handles.FilteringEditorIllumina);
function cancelButton_Callback(hObject, eventdata, handles)
% Resume defaults
handles.alphalims=[0.04 0.06];
handles.margasabs=true;
handles.iqr=[];
handles.var=[];
handles.inten=[];
handles.custom='';
handles.export=false;
handles.usewaitbar=true;
handles.nofilt=false;
handles.invert=false;
handles.outlierTest='none';
handles.pval=[];
handles.dishis=false;
handles.cancel=true; % User pressed cancel
guidata(hObject,handles);
uiresume(handles.FilteringEditorIllumina);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%% HELP FUNCTIONS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function allok = checkExpression(expr)
% PL : Present Calls Lower Alpha
% PU : Present Calls Upper Alpha
% IR : Interquartile Range
% VR : VaRiance
% IN : Intensity
% % PM : Perfect Match Intensity
% % MM : MisMatch Intensity
% If the expression is OK allok is true else false
allok=true;
% Form error messages
errmsg1={'Your filter expression is probably malformed.',...
'Please check your expression again.'};
% Preallocate some random numbers to check the validity of the expression
pl=1;
pu=1;
ir=1;
vr=1;
in=1;
expr=strrep(expr,'*','.*');
expr=strrep(expr,'/','./');
expr=strrep(expr,'=','==');
expr=strrep(expr,'PL','pl');
expr=strrep(expr,'PU','pu');
expr=strrep(expr,'IR','ir');
expr=strrep(expr,'VR','vr');
expr=strrep(expr,'IN','in');
expr=[expr ';'];
try
eval(expr);
catch
allok=false;
uiwait(errordlg([errmsg1,lasterr],'Bad Input','modal'));
end
function checkCheck(stru)
if get(stru.pCallCheck,'Value')==0 && get(stru.iqrCheck,'Value')==0 && ...
get(stru.varCheck,'Value')==0 && get(stru.intenCheck,'Value')==0 && ...
get(stru.customCheck,'Value')==0 && get(stru.nofiltCheck,'Value')==0
set(stru.okButton,'Enable','off')
else
set(stru.okButton,'Enable','on')
end