Filtering a Counts Matrix File

Filtering should be done before normalization. There are three different filtering options available in detk. nonzero, mean, and median. Command line arguments for filter take this form:

detk-filter [options] <filter commands> [--column-data=<column data fn>] <counts_fn>

The structure of the filter command is as follows..

<function>(all or condition) <inequality> <number>

So to if you wanted to only keep rows in the matrix where the means where greater than 10, you would specify

'mean(all)>10'

On the command line. Spacing does not matter and 'mean(all) > 10' is functionally equivalent to the previous command.

Example:

detk-filter -o MyFilteredCounts 'mean(all)>10' MyCounts

Note:

The command describes keeping rows based on meeting the above condition. A csv file is created when specifying output with -o

More detailed information on other methods can be found in the filter.rst file.