The 00_runall.sh will run everything - i.e. FlowSOM 1 and 2 will be run with 4000 different configurations. The script is set up to run on Computerome 1.0 and should be run from the scripts folder.
Step 1:
Make a grid of parameters to be evaluated:
$ Rscript 01_make_parameter_grid.R
Step 2:
Run FlowSOM - The programs run 10 iterations of the clustering algorithm with varying seed.
There are two versions of FlowSOM. Flowsom1 resample the subsample using a varying seed, but keeps the clustering seed constant. Flowsom2, on the other hand, keeps the subsample stable, but varies the seed used for clustering.
$ Rscript 02_flowsom.R -p $PBS_ARRAYID
$ Rscript 02_flowsom2.R -p $PBS_ARRAYID
The variable PBS_ARRAYID refers to the job array values. If a specific parameter set is desired to be run, the position in parameter grid can be used. The function 'file2param' can be used for this. The input is a filename - an example is:
'flowsom1_001_42_1e+05_16.RData'.
> file2param("<flowsom-version>_<patient>_<seed>_<sample-size>_<nclust>.RData")
Step 3:/
Evaluate the generated results and combine them into a single file.
$ echo ../results/02_flowsom1/ | Rscript 03_computeEvaluation.R -f ../results/03_flow1Result.RData
$ echo ../results/02_flowsom2/ | Rscript 03_computeEvaluation.R -f ../results/03_flow2Result.RData
Step 4:
Create various graphs for analysis.
$ Rscript 04_resultAnalysis.R