otu.association

The otu.association command calculate the correlation coefficient for the otus in a shared/relabund file.

Default settings

The otu.association command reads a shared or relabund file.

mothur > otu.association(shared=final.an.0.03.subsample.0.03.pick.shared)

or

mothur > otu.association(relabund=final.an.0.03.subsample.0.03.pick.relabund)

The output file will look like:

OTUA   OTUB    spearmanCoef    Significance
Otu002 Otu001  -0.066667   0.841481
Otu003 Otu001  -0.006061   0.985494
Otu003 Otu002  0.006061    0.985494
Otu004 Otu001  -0.151515   0.649436
Otu004 Otu002  0.078788    0.813151
Otu004 Otu003  0.903030    0.000344
Otu005 Otu001  -0.127273   0.702596
Otu005 Otu002  -0.636364   0.047890
Otu005 Otu003  -0.284848   0.392803
...

Options

groups

The groups parameter allows you to specify which of the groups you would like included. The group names are separated by dashes. By default all groups in the shared or relabund file are used.

label

The label parameter allows you to select what distance level you would like used, if none is given all labels are processed.

method

The method parameter allows you to select what method you would like to use. Options are pearson (default), spearman and kendall.

To use the spearman method:

mothur > otu.association(shared=final.an.0.03.subsample.0.03.pick.shared, method=spearman)

or to use the kendall method:

mothur > otu.association(shared=final.an.0.03.subsample.0.03.pick.shared, method=kendall)

metadata

The metadata parameter allows you to find the association between the otus and the metadata.

mothur > otu.association(shared=final.an.0.03.subsample.0.03.pick.shared, metadata=mouse.dpw.metadata)

cutoff

The cutoff parameter allows you to set a pvalue at which the otu will be reported.

mothur > otu.association(shared=final.an.0.03.subsample.0.03.pick.shared, metadata=mouse.dpw.metadata, cutoff=0.005)

Revisions