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Remove.otus

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The remove.otus command removes otu labels from *.cons.taxonomy, *.corr.axes, *.otu.corr, shared and list files. This can be useful especially with subsampled datasets or when groups have been selected.

Default Options

The remove.otus parameters are: constaxonomy, otucorr, corraxes, shared, list and accnos. The accnos parameter is required as well as at least one of the other file types.

mothur > remove.otus(accnos=final.an.0.03.subsample.0.03.pick.0.03.otus, corraxes=final.an.0.03.subsample.0.03.pick.pearson.corr.axes)

This command will create a final.an.0.03.subsample.0.03.pick.pearson.corr.pick.axes containing the otus NOT in the accnos file.

Options

constaxonomy

The constaxonomy parameter is used to input the results of the classify.otu command.

mothur > remove.otus(accnos=final.an.0.03.subsample.0.03.pick.0.03.otus, constaxonomy=final.an.0.03cons.taxonomy)

The final.an.0.03cons.taxonomy contains 684 otus, but the remove.otulabels command selected the 86 otus NOT in the accnos file.

otucorr

The otucorr parameter is used to input the results of the otu.association command.

mothur > remove.otus(accnos=final.an.0.03.subsample.0.03.pick.0.03.otus, otucorr=final.an.0.03.subsample.0.03.pick.0.03.pearson.otu.corr)


corraxes

The corraxes parameter is used to input the results of the corr.axes command.

mothur > remove.otus(accnos=final.an.0.03.subsample.0.03.pick.0.03.otus, corraxes=final.an.0.03.subsample.0.03.pick.pearson.corr.axes)


list

The list parameter allows you to input a list file you wish to select OTUs from.


shared

The shared parameter allows you to input a shared file you wish to select OTUs from.

mothur > remove.otus(shared=abrecovery.an.shared, groups=B)

Revisions

  • 1.26.0 - First Introduced
  • 1.30.0 - Added list and shared parameters
  • 1.37.0 - Remove.otulabels name changed to remove.otus