Commit bdfe1951 authored by Maximilian Beckers's avatar Maximilian Beckers
Browse files

update readme

parent bc78fac9
......@@ -100,46 +100,6 @@ python /path/to/ -em -p 1.2156
The expected run time on normal desktop computer should be around 1-2 minutes for this example.
## List of options
### Required paramters
-em EM map Example: -em yourEMmap.mrc
-p pixel size Example: -p 1.06
### Optional parameters
-locResMap local resolution map for local filtering Example: -locResMap yourLocalResolutions.mrc
-mm model map for LocScale Example: -mm yourModelMap.mrc
-w window size for background noise estimation Example: -w 50
-noiseBox box coordinates for background noise estimation Example: -noiseBox 50 150 150
-method: method for error control, 'BH' for Benjamini-Hochberg FDR-control, 'BY' for Benjamini-Yekutieli FDR-control (default) or 'Holm' for Holm FWER-control
-w_locscale window size for LocScale Example: -w_locscale 15
-stepSize step size for LocScale Example: -stepSize 5 (default)
-ecdf use ECDF instead of Gaussian CDF for p-value calculation Example: -ecdf
-o filename for output Example: -o out.mrc
-testProc use right-, left- or two-sided testing i.e. 'rightSided', 'leftSided'or 'twoSided' Example: -testProc 'rightSided'
-fdr threshold confidence map at the desired FDR Example: -fdr 0.01
-mpi MPI parallelisation for LocScale Example: -mpi
-lowPassFilter resolution in Angstrom to low-pass filter the map before multiple testing Example: -lowPassFilter 5
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