Table 1 Description of each baseline method included in the benchmark
Name | RNA_wICA | RNA_wNMF | DNAm_EDec | DNAm_MeDeCom | DNAm_wICA | both_wICA | both_wNMFMeDeCom | both_meanwNMFMeDeCom |
|---|---|---|---|---|---|---|---|---|
Acronym | r_WIC | r_WNM | m_EDC | m_MDC | m_WIC | b_WIC | b_COM | b_MEA |
Data type | RNA | RNA | DNAm | DNAm | DNAm | both | both | both |
Feature Selection DNAm | / | / | 5.000 most variable probes | 5.000 most variable probes | 5.000 most variable probes | 5.000 most variable probes | 5.000 most variable probes | 5.000 most variable probes |
Feature Selection RNA | ICA, selection of top-contributing genes and filtering of duplicated genes | ICA, selection of top-contributing genes | / | / | / | / | ICA, selection of top-contributing genes | ICA, selection of top-contributing genes |
Deconvolution algorithm DNAm | / | / | Edec | MeDeCom | ICA weighted by top-contributing probes | ICA weighted by top-contributing probes | MeDeCom with the A matrix computed on RNA as startA parameter | MeDeCom |
Deconvolution algorithm RNA | ICA weighted by top-contributing genes | NMF with snmf/r method | / | / | / | ICA weighted by top-contributing genes | NMF with snmf/r method | NMF with snmf/r method |
Multi-omic integration strategy | / | / | / | / | / | Averaged DNAm and RNAm proportion matrix | DNAm deconvolution uses RNA deconvolution as input | Averaged DNAm and RNAm proportion matrix |
Time 10 A | ~ 10 min | ~ 20 min | ~ 3 h | ~ 17 h | ~ 10 min | ~ 10 min | ~ 17 h | ~ 17 h 30 min |
Time 1 A | ~ 1 min | ~ 2 min | ~ 20 min | ~ 1 h 40 | ~ 1 min | ~ 1 min | ~ 1 h 40 min | ~ 1 h 45 min |
Reference of the tools/algorithms used | Hyvarinen [25] | Frichot et al. [26] | Onuchic et al. [9] | Lutsik et al. [8] | Hyvarinen [25] | Hyvarinen [25] |