We will be offering mothur and R workshops throughout 2019. Learn more.

Difference between revisions of "Sparcc"

From mothur
Jump to: navigation, search
(Revisions)
(Revisions)
Line 45: Line 45:
 
* 1.31.0 - First Introduced
 
* 1.31.0 - First Introduced
 
* 1.39.0 - Fixes floating point exception
 
* 1.39.0 - Fixes floating point exception
 +
* 1.40.0 - Speed and memory improvements for shared files. [https://github.com/mothur/mothur/issues/357 #357] , [https://github.com/mothur/mothur/issues/347 #347]
  
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Revision as of 14:31, 29 March 2018

The sparcc command allows you to .... To run this tutorial please download: fake_data.1.subsample.shared.zip.


Default

The shared parameter is required.

mothur > sparcc(shared=fake_data.1.subsample.shared)

Options

samplings

The samplings parameter is used to .... Default=20.

mothur > sparcc(shared=fake_data.1.subsample.shared, samplings=10)

iterations

The iterations parameter is used to ....Default=10.

mothur > sparcc(shared=fake_data.1.subsample.shared, iterations=100)

permutations

The permutations parameter is used to ....Default=1000.

mothur > sparcc(shared=fake_data.1.subsample.shared, permutations=10000)

method

The method parameter is used to ....Options are relabund and dirichlet. Default=dirichlet.

mothur > sparcc(shared=fake_data.1.subsample.shared, method=relabund)

groups

The groups parameter is used to select groups from your shared file. The default value for groups is all the groups in your shared file. Group names may be separated by dashes.

mothur > sparcc(shared=fake_data.1.subsample.shared, groups=0-1-2)

label

The label parameter is used to analyze specific labels in your shared file.

processors

The processors parameter allows you to run the command with multiple processors. The default processors is 1.

mothur > sparcc(shared=fake_data.1.subsample.shared, processors=2)

Revisions

  • 1.31.0 - First Introduced
  • 1.39.0 - Fixes floating point exception
  • 1.40.0 - Speed and memory improvements for shared files. #357 , #347