% script that demonstrates cross annotation of the
% two experiments provided here as tutorial example.
% the script assumes that the script file resides
% with all data described in README in the current directory
% It will also require that the current directory is 
% the base directory of all necessary libraries.
% This is how the install script will place the files
% automatically. If the actuall setup differs, one must
% adjust all addpath statements.
% 
% (C) P. Sykacek 2005, 2006 <peter@sykacek.net>

addpath('./mca_fuse/')
addpath('./helpers/')
addpath('./mca_base/')
% cross anotation is here based on "siumulated" cross annotation information
% note that the first column shows some of NIA's murine id's and the second 
% artificially generated id's
cdef.cfname=['./crossann.tsv'];
% we have two different species here (NIA and simulated)
cdef.nspec=2;
% log file that stores this cross annotation structure
cdef.logfile=['./crosslog.mat'];
% first column refers to the NIA id's which we use as target annotations.
cdef.targspecdx=1;
% file name that contains the three column gene specification 
% (gene id, gene symbol and extended gene specification)
% for all possible target id's (before cross annotation)
cdef.gspcifnam=['./genespec.csv'];
cdef.gspccols={'GENEID', 'Gene Symbol', 'Gene description'};
% file name that contains the three column gene specification 
% (gene id, gene symbol and extended gene specification)
% for the cross annotated target id's in correct order for all species!
cdef.gspcofnam=['./crossanngenespec.mat'];
cdef.donormalise=1;
% experiments description:
% first entry: exp1
% this is already annoptated by target id's and cross annotation only filters and
% reorders the data.
cdef.exps(1).mcafname=['./exp1mca.tsv'];
cdef.exps(1).trgfname=['./exp1eff.tsv'];
% we do not extract separate training and test samples.
cdef.exps(1).trandx=nan;
cdef.exps(1).tstdx=nan;
% column number of the gene ids of this experiment in the
% cross annotation file.
cdef.exps(1).srcspec=1;
cdef.exps(1).datafnam=['./exp1.mat'];
% second entry: exp2
% this experiment uses hypothetical gene ids and will be cross annotated to the
% NIA' ids.
cdef.exps(2).mcafname=['./exp2mca.tsv'];
cdef.exps(2).trgfname=['./exp2eff.tsv'];
% we do not extract separate training and test samples.
cdef.exps(2).trandx=nan;
cdef.exps(2).tstdx=nan;
% column number of the gene ids of this experiment in the
% cross annotation file.
cdef.exps(2).srcspec=2;
cdef.exps(2).datafnam=['./exp2.mat'];
% finally we run cross annotation
cdef=newcrossan(cdef);