Extend functionality to arbitrary number of matrices (beyond methylation and coverage)

Cellular-Longevity / cmapR

Tools for manipulating annotated data matrices

BSD 3-Clause "New" or "Revised" License

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Extend functionality to arbitrary number of matrices (beyond methylation and coverage) #1

Closed bsiranosian closed 2 years ago

bsiranosian commented 2 years ago

Decided that this is going to remain fixed with methylation and coverage for the time being, because there isn't any immediately apparent other use cases. The address syntax mgct@meth_mat will remain.

However, the internal representation in the hdf5 object will change to use a 3D array rather than separate methylation and coverage matrices. Then portability across datasets is easier.

bsiranosian commented 2 years ago

Fixed as of bc35e33a2cf3a80eb068f32372d88329986b8559

mGCT objects now write data matrix to 0/DATA/0/MATRIX in the hdf5 file as a 3D array. Dimensions are (rows, columns, meth/cov). Slots in the object remain the same at meth_mat and cov_mat.