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convert_counts_matrix failing with .monoclerc #726

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rfriedman22 opened this issue Jun 12, 2024 · 0 comments
Open

convert_counts_matrix failing with .monoclerc #726

rfriedman22 opened this issue Jun 12, 2024 · 0 comments
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@rfriedman22
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The develop branch has been updated to source a $HOME/.monoclerc file on load. However, when I call convert_counts_matrix(cds) with no additional arguments, I get the following error because the matrix_control parameter is an empty list:

Error: convert_counts_matrix: invalid matrix_control parameter

I was able to solve it by setting the matrix_control argument to the value set in my rcfile:

convert_counts_matrix(cds, matrix_control = monocle3:::get_global_variable("matrix_control_bpcells_unrestricted"))

I think that this function should look for the global parameter if nothing is specified by the user as input to convert_counts_matrix().

@rfriedman22 rfriedman22 added the bug Something isn't working label Jun 12, 2024
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