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Difference between revisions of "Sens.spec"

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==Default Parameters==
 
==Default Parameters==
  
  mothur > sens.spec(list=96_lt_column_amazon.fn.list, column=96_lt_column_amazon.dist)
+
  mothur > sens.spec(list=96_lt_column_amazon.fn.list, column=96_lt_column_amazon.dist, name=amazon.names)
 +
 
 +
or
 +
 
 +
mothur > sens.spec(list=96_lt_column_amazon.fn.list, column=96_lt_column_amazon.dist, count=amazon.count_table)
  
 
or
 
or
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==Options==
 
==Options==
 +
 +
===name===
 +
The name parameter allows you to enter a name file associated with your distance matrix.
 +
 +
===count===
 +
The count parameter allows you to enter a count file associated with your distance matrix.
  
 
===hard===
 
===hard===
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* 1.23.0 - fixed label option and added smart distancing.  
 
* 1.23.0 - fixed label option and added smart distancing.  
 
* 1.29.0 - increased speed and reduced memory required.
 
* 1.29.0 - increased speed and reduced memory required.
 
+
* 1.38.0 - added count parameter
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Latest revision as of 17:09, 20 July 2016

The sens.spec command...

Default Parameters

mothur > sens.spec(list=96_lt_column_amazon.fn.list, column=96_lt_column_amazon.dist, name=amazon.names)

or

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

name

The name parameter allows you to enter a name file associated with your distance matrix.

count

The count parameter allows you to enter a count file associated with your distance matrix.

hard

precision

cutoff

label

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