Added two arguments to EpiMutations():
sample_id (str): The colname in case to compute epimutations on.
cases_as_controls (bool): Should remaining cases be used as controls?
Proposed solution involves the following:
Before concatenating cases and controls, add an "origin" column in pData which equals "case" or "control". This marks each sample's origin.
Concatenate cases and controls into a single set.
If cases_as_control is False, keep only columns in set where origin="control" or colname="sample_id".
If cases_as_control is True, do not remove anything. The remaining cases are automatically considered as controls in the downstream code.
Added two arguments to
EpiMutations():sample_id(str): The colname incaseto compute epimutations on.cases_as_controls(bool): Should remaining cases be used as controls?Proposed solution involves the following: