Package: M3JF 0.1.0

Xiaoyao Yin

M3JF: Multi-Modal Matrix Joint Factorization for Integrative Multi-Omics Data Analysis

Multi modality data matrices are factorized conjointly into the multiplication of a shared sub-matrix and multiple modality specific sub-matrices, group sparse constraint is applied to the shared sub-matrix to capture the homogeneous and heterogeneous information, respectively. Then the samples are classified by clustering the shared sub-matrix with kmeanspp(), a new version of kmeans() developed here to obtain concordant results. The package also provides the cluster number estimation by rotation cost. Moreover, cluster specific features could be retrieved using hypergeometric tests.

Authors:Xiaoyao Yin [aut, cre]

M3JF_0.1.0.tar.gz
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13 exports 0.00 score 54 dependencies 2 scripts 176 downloads

Last updated 1 years agofrom:796c977d15. Checks:OK: 2. Indexed: yes.

Exports:costcrimmix_data_genfeature_screen_sdfeature_selectioninitialize_WLiNMF_data_genintersim_data_genkmeansppM3JFRotationCostBestGivenGraphsimulateYupdate_Eupdate_H

Dependencies:alluvialBiobaseBiocGenericsBiocManagercliclustercodetoolscolorspacedigestdoParalleldplyrExPositionfansifarverforeachgenericsggplot2gluegridBasegtableInterSIMisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmeNMFpillarpkgconfigplyrprettyGraphsR6RColorBrewerRcppregistryreshape2rlangrngtoolsscalesSNFtoolstringistringrtibbletidyselectutf8vctrsviridisLitewithr