sens.spec
The sens.spec command...
Default Parameters
mothur > sens.spec(list=96_lt_column_amazon.fn.list, column=96_lt_column_amazon.dist, count=amazon.count_table)
or
mothur > sens.spec(list=96_lt_column_amazon.fn.list, phylip=98_lt_phylip_amazon.dist)
If you open 96_lt_column_amazon.fn.sensspec, you would see:
label cutoff tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
unique unique 2 4751 0 0 1 1 1 1 0 1 1 1
0.00 0.00 3 4750 0 0 1 1 1 1 0 1 1 1
0.01 0.01 5 4746 0 2 0.7143 1 1 0.9996 0 0.9996 0.845 0.8333
0.02 0.02 14 4737 0 2 0.875 1 1 0.9996 0 0.9996 0.9352 0.9333
0.03 0.03 21 4732 0 0 1 1 1 1 0 1 1 1
0.04 0.04 24 4728 0 1 0.96 1 1 0.9998 0 0.9998 0.9797 0.9796
0.05 0.05 34 4717 0 2 0.9444 1 1 0.9996 0 0.9996 0.9716 0.9714
Options
count
The count parameter allows you to enter a count file associated with your distance matrix.
hard
precision
cutoff
label
name - not recommended
The name parameter allows you to enter a name file associated with your distance matrix.
Revision
- 1.23.0 - fixed label option and added smart distancing.
- 1.29.0 - increased speed and reduced memory required.
- 1.38.0 - added count parameter
- 1.47.0 - Fixes bug in sens.spec when name file is used