I am trying to run methylprep process from the command line without poobah filtering. Documentation says:
--poobah By default, any beta-values or m-values output will
contain all probes. If True, those probes that fail
the p-value signal:noise detection are replaced with
NaNs in dataframes in beta_values and m_value output.
It also states that --poobahis a Boolean variable with default True. This suggests that if I would like a beta_values output without poobah filtering I should add the option --poobah False to the methylprep process command. However, when I do this I get the error:
[Error]:
unrecognized arguments: False
How can I switch poobah filtering off in the command line?
Can I also confirm that the CSV file named something like "200772300016_R01C01_processed.csv" in a folder called "200772300016" contains all beta-values etc without any filtering?
I am trying to run methylprep process from the command line without poobah filtering. Documentation says:
It also states that
--poobahis a Boolean variable with default True. This suggests that if I would like a beta_values output without poobah filtering I should add the option--poobah Falseto themethylprep processcommand. However, when I do this I get the error:How can I switch poobah filtering off in the command line?
Can I also confirm that the CSV file named something like "200772300016_R01C01_processed.csv" in a folder called "200772300016" contains all beta-values etc without any filtering?