More options for otu.association

Feature requests
1

I suggest to add sort option (for p-value) and cutoff (otu pairs higher than 0.05 p-value can be discarded) for otu.association command. I have over 1500 otus and the list is quite long, so it is hard to manually sort it.

2

This will be in 1.28.0.

3

Hi,

Is there an option for specifying which OTU’s to use in the otu.association command. I have about ~4500 OTUs (15 month temporal dataset), but am only interested in otu.association results for OTUs that make up more than 1% of any given sample or for the ones that appear in >90% of the samples.

Thanks very much,
Ameet

4

Probably not essential, but would be a nice feature in the future for otu.association to include options to transform the data? for example otu.association(shared=file.subsample.shared, transform=log(1+x)).

Thanks,
Ameet

5

Ameet - you should try filter.shared to filter your shared file as desired.

6

Thanks very much Pat. Was not aware of this command - makes things very convenient.

Thanks again,
Ameet