Using SigProfilerTopography Output
This section goes over the different directories and files that are generated when running SigProfilerTopography. The example directories throughout this section were generated from the Quick Start Example.
Output Overview¶
The output directory results/21BRCA_SPT will contain subdirectories data, figure, SPA, and logs. Below is a preliminary view of the directories that will be generated in results/21BRCA_SPT.
data¶
Under the data directory, data files and subdirectories containing analysis specific data files are created while conducting topography analyses, and these files are used while plotting figures.
data files¶
Table_SBS_Signature_Cutoff_NumberofMutations_AverageProbability.txt is an exampler data file that contains all the information about the SBS mutational signatures considered in the topography analyses.
The main columns of the file include the following: - jobname (here shown as cancer_type) - signature - cutoff - number_of_mutations - average_probability - samples_list - len(samples_list) - len(all_samples_list) - percentage_of_samples
Below is an example of what the file contains:
figure¶
Under figure directory, there will be subdirectories for each topography analysis containing resulting plots.
To learn more about the contents of each of the subdirectories, refer to their corresponding sections:
Nucleosome Occupancy: Output - Nucleosome Occupancy
Replication Timing: Output - Replication Timing
Strand Asymmetry: Output - Strand Asymmetry
Epigenomics Occupancy: Output - Epigenomics Analysis
Strand-coordinated Mutagenesis (processivity): Output - Strand-coordinated Mutagenesis
logs¶
Under logs directory, you will find the log files. An example of the layout of the logs directory is:
SPA¶
If you run SigProfilerTopography without providing probability matrices, SigProfilerTopography utilizes SigProfilerAssignment by default to attribute the activities of known reference mutational signatures from the Catalogue Of Somatic Mutations In Cancer (COSMIC) database to each examined sample. An example of the layout of the SPA directory is:
Output for SigProfilerTopography run with probability matrices¶
However, if you run SigProfilerTopography with probability matrices, SigProfilerAssignment will not be executed. Therefore, there won't be any SPA subdirectory. The output directory results/21BRCA_SPT_with_probability_matrices will contain subdirectories data, figure, and logs. Layout of these subdirectories will be the same.