This tool statistically evaluates differences in genomic features between groups of regions along the genome. In particular, it implements the Interval-Wise Testing for omics data, an extended version of the Interval-Wise Testing for functional data presented in Pini and Vantini (2017). It allows to perform multiple two sample permutation tests between pairs of region datasets, on several features. It returns the adjusted p-value curves for every test and all possible scales. Moreover, it creates a graphical representation of the Interval-Wise Testing results and a summary plot (optional) with p-values at the maximum scale. The tool IWTomics Plot with Threshold on Test Scale permits to select the scale to be used in the plots.

Input files

RData file with the IWTomicsData object, tabular files with region dataset IDs and feature IDs. These files are created by the tool IWTomics Load Smooth and Plot.

Output

The tool returns:

1. TXT file with an adjusted p-value matrix for every test performed. Each matrix contains a p-value curve (row) for every scale considered in the test;
2. PDF file with the plotted test results;
3. PDF file with the summary plot;
4. RData with the IWTomicsData object with the test results;
5. Test identifiers;
6. Feature identifiers.

4-6 can be used as input of the tool IWTomics Plot with Threshold on Test Scale

Notes

This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).

It implements a simplified version of the function IWTomicsTest, plotTest and plotSummary for IWTomicsData objects. The complete version can be found in the R/Bioconductor package IWTomics (see vignette).