SlipGURU Dipartimento di Informatica e Scienze dell'Informazione Università Degli Studi di Genova

v1vs2 Package

v1vs2 Package

Provides tool scripts used for comparison of output generated by KDVS between two versions: earlier (dubbed v1) and current (dubbed v2). KDVS v1 was published along with [Z2013]:

[Z2013]G Zycinski, A Barla, M Squillario, T Sanavia, B Di Camillo, A Verri, “Knowledge Driven Variable Selection (KDVS) - a new approach to enrichment analysis of gene signatures obtained from high-throughput data”, Source Code Biol Med 8 (2013), no. 1, 2 (http://www.scfbm.org/content/8/1/2)

All file paths are hard–coded. Unless stated otherwise, all scripts shall pass silently; in case of an error, AssertionError is raised.

countvars Module

Check if variables are counted in exactly the same way for both L1L2_L1L2 and L1L2_OLS. NOTE: there is known discrepancy between v1 and v2 regarding how variables coming from ‘not selected’ data subsets are counted. See InnerSelector_ClassificationErrorThreshold_L1L2_VarsFreq for more details.

kdvs.tools.v1vs2.countvars.main()

err_stats Module

Check if all statistical details of L1L2_L1L2 are reported in the same way (up to those elements that are present in both v1 and v2).

kdvs.tools.v1vs2.err_stats.main()

freqvars_l1l2 Module

Check if all frequencies for variables are calculated correctly for L1L2_L1L2. NOTE: there is known discrepancy due to relative order of variables that share the same frequency; this has been addressed by comparing in sets.

kdvs.tools.v1vs2.freqvars_l1l2.main()

freqvars_ols Module

Check if all frequencies for variables are calculated correctly for L1L2_OLS. NOTE: there is known discrepancy due to relative order of variables that share the same frequency; this has been addressed by comparing in sets.

kdvs.tools.v1vs2.freqvars_ols.main()

subsets Module

Check that all generated subset information is the same.

kdvs.tools.v1vs2.subsets.main()

utl Module

Check if UTL (unified term lists) for L1L2_L1L2 and L1L2_OLS are reported in the same way. See L1L2_PKC_UTL_Reporter for more details. NOTE: there is known discrepancy due to different versions of Gene Ontology release; this has been addressed by printing those differences and manual verification.

kdvs.tools.v1vs2.utl.main()

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