Description Usage Arguments Value
Preparation of elements and active sites for ActiveDriverWGS analysis with the find_drivers
function
1 2 | prepare_elements(elements_file, sites_file, window_size = 50000,
mc.cores = 1, recovery_dir = NA)
|
elements_file |
path to a BED12 file of the elements to analyze |
sites_file |
path to a BED4 file of active sites to use in the analysis |
window_size |
numeric value for the size of the background sequence window to use on each side of the given elements. Default value is 50000. |
mc.cores |
numeric indicating the number of computing cores to use. Default value is 1. |
recovery_dir |
path to a directory for ActiveDriverWGS to store intermediate computations in. In the case that prepare_elements does not complete, run it again with the same value for this parameter, and it will read the intermediate computations rather than compute them again. Please specify a different directory, or delete the ActiveDriverWGS data in a previously used directory, if running with different data. Default value is NA, and prepare_elements will not save any intermediate information with this value. |
list containing element and active site information needed for ActiveDriverWGS analysis
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