gadagui.exe -- imports an input text file and runs the SBL algorithm.
smallexample.txt -- example input text file for gadagui.exe
gadareport.exe -- runs the Backward Elimination algorithm and reports CNA
smallexample.mat -- example input text file for gadareport.exe
Usage example:
Prepare <inputfile.txt> with the data with the same format as smallexample.txt;
i.e. a tab delimited file with:
Probeid Sample1 ... SampleN ChrNum Position
Run gadagui.exe which calls the GADA algorithm:
Select input file <inputfile.txt>
Set output file name <result.mat>
Specify algorithm parameters:
a -- SBL hyperprior parameter
T -- Minumum T for the Backward Elimination
M -- Minimum amount of probes in the segments
Run gadareport.exe; i.e. BE adjustment, visualitzation, and CNA report:
Select mat file <result.mat>
Adjust BE algorithm parameters
(parameters cannot be adjusted to a smaller setting than the one
that was used in gadagui.exe):
T -- T for the Backward Elimination
M -- Minimum amount of probes in the segments
