Package: M2SMF 2.0
M2SMF: Multi-Modal Similarity Matrix Factorization for Integrative Multi-Omics Data Analysis
A new method to implement clustering from multiple modality data of certain samples, the function M2SMF() jointly factorizes multiple similarity matrices into a shared sub-matrix and several modality private sub-matrices, which is further used for clustering. Along with this method, we also provide function to calculate the similarity matrix and function to evaluate the best cluster number from the original data.
Authors:
M2SMF_2.0.tar.gz
M2SMF_2.0.zip(r-4.5)M2SMF_2.0.zip(r-4.4)M2SMF_2.0.zip(r-4.3)
M2SMF_2.0.tgz(r-4.4-any)M2SMF_2.0.tgz(r-4.3-any)
M2SMF_2.0.tar.gz(r-4.5-noble)M2SMF_2.0.tar.gz(r-4.4-noble)
M2SMF_2.0.tgz(r-4.4-emscripten)M2SMF_2.0.tgz(r-4.3-emscripten)
M2SMF.pdf |M2SMF.html✨
M2SMF/json (API)
| # Install 'M2SMF' in R: |
| install.packages('M2SMF', repos = c('https://yinxy1992.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 5 years agofrom:c11364b28b. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 26 2024 |
| R-4.5-win | OK | Aug 26 2024 |
| R-4.5-linux | OK | Aug 26 2024 |
| R-4.4-win | OK | Aug 26 2024 |
| R-4.4-mac | OK | Aug 26 2024 |
| R-4.3-win | OK | Aug 26 2024 |
| R-4.3-mac | OK | Aug 26 2024 |
Exports:affinityMatrixCal_NMIcostdist2bindist2chidist2euinitializationinitialize_WLM2SMFnew_modularitysimu_data_genStandard_Normalizationupdate_alphaupdate_L
Dependencies:clidplyrfansigenericsgluelifecyclemagrittrMASSpillarpkgconfigR6rlangtibbletidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| To calculate the similarity matrix | affinityMatrix |
| calculate the normalized mutual information. | Cal_NMI |
| Calculate the cost | cost |
| Calculate the agreement-based measurement | dist2bin |
| Calculate the chi-squared distance | dist2chi |
| Calculate the Euclidean distance | dist2eu |
| initialize the sub-matrix Ci into alpha*Li by SVD | initialization |
| Initialize from the similairty matrix list | initialize_WL |
| the main part for M2SMF and clustering result | M2SMF |
| Calculate the modularity | new_modularity |
| Generate simulated data | simu_data_gen |
| Normalize the input matrix by column | Standard_Normalization |
| the function to update alpha | update_alpha |
| the function to update Li, for i=1,2,...,N | update_L |
