Expected Results

A successful PGS execution will generate a result/ folder which composed of 4 subfolders:

• probMat/ : contains the input hdf5 TAD-TAD probability matrix (if option 1 or 2 is used).
• actDist/ : contains intermediate files generated by A-step (restraint assignment step). A file is generated at each A/M iteration, and will be used in the subsequent M-step (model optimization).
• structure/ : contains structure information files. One .hms file has snapshot coordinates of a model with different optimization steps depending on theta parameters.
• report/ : contains preliminary analysis with some plots.

The following we describe results under report/ folder.

heatmap

Contains genome-wide heat map plots of contact probabilities, calculated from both the model population and experiment data (input matrix). A figure showing density scatter plots (log-log scale) as a comparison between them is also provided.

intraMatrix

Contains heat map plots of contact probabilities for every chromosome, calculated from both the model population and experiment data (input matrix).

radialPlot

Contains scater plots of mean radial position of all TADs, organized by chromosomes in pdf files. The mean radial positions are also recorded in a text file radialPlot_summary.txt.

violations

Contains a text file that tells the average portion of violated restraints per model.