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maqin2001 / qubic-r-package

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Add parameter and documents to scgraph #4

Closed maqin2001 closed 6 years ago

maqin2001 commented 6 years ago

update 04-10-2018

  1. Column and row names need to be added.
  2. Add code to change diagonal to 0. Maybe simply add: diag(mat) <- 0
zy26 commented 6 years ago

@maqin2001, more tests and documents are needed.

PegasusAM commented 6 years ago

I used: mat <- scgraph(bic,cleardiagonal = TRUE, dimnames = NULL) no change for the diagonal

For cell name assignment, it is required rather than a function option. It should be directly from biclustering and exactly matched with the values in graph matrix, because we need to take consideration of the situation that the biclusters do not include all cells. Otherwise, we have no idea which cells are excluded and directly affect all following steps.

zy26 commented 6 years ago

The problem with cleardiagonal was fixed in 476c0f0. Currently, the result of scgraph does include all cells. We can add another function to remove unused cells.