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Difference between revisions of "Normalize.shared"

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The normalize.shared command can only be executed after a successful read.otu command of a list and group or shared file. It creates a .norm.shared file.
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The normalize.shared command creates a .norm.shared file.
  
 
__TOC__
 
__TOC__
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By default, the method is totalgroup, the norm is set to the number of sequences in your smallest group, all groups in your group file are included and all labels are used.
 
By default, the method is totalgroup, the norm is set to the number of sequences in your smallest group, all groups in your group file are included and all labels are used.
 
   
 
   
  mothur > normalize.shared()
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  mothur > normalize.shared(shared=abrecovery.fn.shared)
  
  
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The groups parameter allows you to select the groups you would like to include in your .norm.shared file.
 
The groups parameter allows you to select the groups you would like to include in your .norm.shared file.
  
  mothur > normalize.shared(groups=B-C)
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  mothur > normalize.shared(shared=abrecovery.fn.shared, groups=B-C)
  
 
==method==
 
==method==
The method parameter allows you to select what method you would like to use to normalize. The only choice is totalgroup. We hope to add more ways to normalize in the future, suggestions are welcome!
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The method parameter allows you to select what method you would like to use to normalize. The choices are totalgroup and zscore. We hope to add more ways to normalize in the future, suggestions are welcome!
  
 
Relative Abundance = Abundance / Total number of sequences in the group.
 
Relative Abundance = Abundance / Total number of sequences in the group.
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The normalized value is then rounded to the nearest integer.
 
The normalized value is then rounded to the nearest integer.
  
  mothur > normalize.shared(method=totalgroup)
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  mothur > normalize.shared(shared=abrecovery.fn.shared, method=totalgroup)
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or zscore
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Normalized Abundance = (Abundance - mean) / standard deviation
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If using a shared file the normalized value is then rounded to the nearest integer.
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mothur > normalize.shared(shared=abrecovery.fn.shared, method=zscore)
  
 
==norm==
 
==norm==
The norm parameter allows you to number you would like to normalize to. By default this is set to the number of sequences in your smallest group.
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The norm parameter allows you to number you would like to normalize to. By default this is set to the number of sequences in your smallest group.  If you set norm greater than an abundance of a specific group the group will be removed.
  
  mothur > normalize.shared(norm=100)
+
  mothur > normalize.shared(shared=abrecovery.fn.shared, norm=100)
  
 
==label==
 
==label==
 
There may only be a couple of lines in your OTU data that you are interested in finding the normalized abundance for. There are two options. You could: (i) manually delete the lines you aren't interested in from your list file; (ii) or use the label option. To use the label option with the normalize.shared() command you need to know the labels you are interested in. If you want the normalized abundance for the lines labeled unique, 0.03, 0.05 and 0.10 you would enter:
 
There may only be a couple of lines in your OTU data that you are interested in finding the normalized abundance for. There are two options. You could: (i) manually delete the lines you aren't interested in from your list file; (ii) or use the label option. To use the label option with the normalize.shared() command you need to know the labels you are interested in. If you want the normalized abundance for the lines labeled unique, 0.03, 0.05 and 0.10 you would enter:
  
  mothur > normalize.shared(label=unique-0.03-0.05-0.10)
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  mothur > normalize.shared(shared=abrecovery.fn.shared, label=unique-0.03-0.05-0.10)
 +
 
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==makerelabund==
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The makerelabund parameter allows you to convert a shared file to a relabund file before you normalize. default=f.
  
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==Revisions==
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* 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]]

Latest revision as of 14:27, 29 March 2018

The normalize.shared command creates a .norm.shared file.


Default Settings

By default, the method is totalgroup, the norm is set to the number of sequences in your smallest group, all groups in your group file are included and all labels are used.

mothur > normalize.shared(shared=abrecovery.fn.shared)


groups

The groups parameter allows you to select the groups you would like to include in your .norm.shared file.

mothur > normalize.shared(shared=abrecovery.fn.shared, groups=B-C)

method

The method parameter allows you to select what method you would like to use to normalize. The choices are totalgroup and zscore. We hope to add more ways to normalize in the future, suggestions are welcome!

Relative Abundance = Abundance / Total number of sequences in the group. Normalized Value = Relative Abundance * norm The normalized value is then rounded to the nearest integer.

mothur > normalize.shared(shared=abrecovery.fn.shared, method=totalgroup)

or zscore Normalized Abundance = (Abundance - mean) / standard deviation If using a shared file the normalized value is then rounded to the nearest integer.

mothur > normalize.shared(shared=abrecovery.fn.shared, method=zscore)

norm

The norm parameter allows you to number you would like to normalize to. By default this is set to the number of sequences in your smallest group. If you set norm greater than an abundance of a specific group the group will be removed.

mothur > normalize.shared(shared=abrecovery.fn.shared, norm=100)

label

There may only be a couple of lines in your OTU data that you are interested in finding the normalized abundance for. There are two options. You could: (i) manually delete the lines you aren't interested in from your list file; (ii) or use the label option. To use the label option with the normalize.shared() command you need to know the labels you are interested in. If you want the normalized abundance for the lines labeled unique, 0.03, 0.05 and 0.10 you would enter:

mothur > normalize.shared(shared=abrecovery.fn.shared, label=unique-0.03-0.05-0.10)

makerelabund

The makerelabund parameter allows you to convert a shared file to a relabund file before you normalize. default=f.

Revisions

  • 1.40.0 - Speed and memory improvements for shared files. #357 , #347