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

Difference between revisions of "Get.rabund"

From mothur
Jump to: navigation, search
 
Line 3: Line 3:
  
 
==Default==
 
==Default==
If you read in a [[list file]], get.rabund will generate the corresponding rabund file:
+
If you read in a [[list file]], [[shared_file]] or [[sabund_file]], get.rabund will generate the corresponding rabund file:
  
 
  mothur > get.rabund(list=amazon.fn.list)
 
  mothur > get.rabund(list=amazon.fn.list)
Line 10: Line 10:
  
 
  mothur > get.rabund(sabund=amazon.fn.sabund)
 
  mothur > get.rabund(sabund=amazon.fn.sabund)
 +
 +
or
 +
 +
mothur > get.rabund(shared=amazon.an.shared)
  
  
 
==Options==
 
==Options==
===label options===
+
===label===
 
If the list file contains multiple lines and you are only interested in a subset of those lines you can use the label option:
 
If the list file contains multiple lines and you are only interested in a subset of those lines you can use the label option:
  
 
  mothur > get.rabund(list=amazon.fn.list, label=unique-0.03-0.10-0.20)
 
  mothur > get.rabund(list=amazon.fn.list, label=unique-0.03-0.10-0.20)
  
===sorted option===
+
===sorted===
 
By default the data in the rabund file are not sorted.  That is they are in the same order as the OTUs in your list file.  If you would like these data to be sorted by their abundance you need to use the sorted option:
 
By default the data in the rabund file are not sorted.  That is they are in the same order as the OTUs in your list file.  If you would like these data to be sorted by their abundance you need to use the sorted option:
  
 
  mothur > get.rabund(list=amazon.fn.list, sorted=T)
 
  mothur > get.rabund(list=amazon.fn.list, sorted=T)
 +
 +
===groups===
 +
You can use the groups parameter to specify which groups you want included in your analysis.
 +
 +
mothur > get.rabund(shared=amazon.shared, groups=pasture)
  
 
===count===
 
===count===
Line 30: Line 39:
 
==Revisions==
 
==Revisions==
 
* 1.31.0 - Added count parameter.
 
* 1.31.0 - Added count parameter.
 +
* 1.41.0 - Adds shared and groups options. [https://github.com/mothur/mothur/issues/325  #325]
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Latest revision as of 19:17, 30 October 2018

The get.rabund command will generate an rabund file based on the OTU data that you have read into mothur.


Default

If you read in a list file, shared_file or sabund_file, get.rabund will generate the corresponding rabund file:

mothur > get.rabund(list=amazon.fn.list)

or

mothur > get.rabund(sabund=amazon.fn.sabund)

or

mothur > get.rabund(shared=amazon.an.shared)


Options

label

If the list file contains multiple lines and you are only interested in a subset of those lines you can use the label option:

mothur > get.rabund(list=amazon.fn.list, label=unique-0.03-0.10-0.20)

sorted

By default the data in the rabund file are not sorted. That is they are in the same order as the OTUs in your list file. If you would like these data to be sorted by their abundance you need to use the sorted option:

mothur > get.rabund(list=amazon.fn.list, sorted=T)

groups

You can use the groups parameter to specify which groups you want included in your analysis.

mothur > get.rabund(shared=amazon.shared, groups=pasture)

count

If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file with the get.rabund command.

mothur > get.rabund(list=amazon.an.unique_list, count=amazon.count_table)

Revisions

  • 1.31.0 - Added count parameter.
  • 1.41.0 - Adds shared and groups options. #325