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

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