Transform otu_table(In absolute Abundance) to relative abundance

[EricG]

Hello Dear Qiimers,

I just wonder if there is a script to transform the otu_table.biom(In absolute Abundance) to otu_table.biom (In relative abundance), or anyone know a fancy way to do it using R (phyloseq->otu_table)

Cheers,

Eric

[Will Van Treuren]

Hi Eric,

QIIME/Biom do not currently have a script which does this conversion. summarize_taxa.py will summarize your otu table and in the process convert to relative abundance, but this will alter the table as it will collapse any otus which have the same taxonomic classification. The operation is very straightforward in python, but I am not sure how you would do it in R. The operation in python is:

from biom.parse import parse_biom_table

bt = parse_biom_table(open('/path/to/your/biom_table.biom')

ra_bt = bt.normSampleByObservation()

ra_bt_str = ra_bt.getBiomFormatJsonString('generated_by_will')

o = open('/path/to/new/biom.biom','w')

o.writelines(ra_bt_str)

o.close()

You should then have your new, relative abundance biom table written out. You can add a feature request for this functionality on the biom format gituhub here.

Best, 

Will 

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[Eric JC Galvez B]

Sorry For the delay delay answer, it is working perfect, thanks a lot :), Just for the people there is one parenthesis left at the end of the second line:),

cheers!

Eric

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[Jennifer]

Hi Will thanks for providing this solution, however the script calculates the relative abundance of each OTU over it's total abundance in all samples instead of the relative abundance of each OTU within each sample. The latter I think is appropriate for most applications.

Take care,

Jen

[Eric JC Galvez]

Hallo Jen,

Thanks for sharing the best way that I found was via R phyloseq

Using 

mysamples_RelAbundance = transform_sample_counts(mysample_phyloseq, function(x) x/sum(x))

It should be implemented in qiime soon and more after this

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003531

Best,

Eric

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     Eric JC Gálvez B.

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[Zoey]

Thanks to Will for the python scripts. 

I would like to mention that this script generates an OTU table with reads per OTU divided by the total counts of that OTU, which is different from reads per OTU in a sample by the total reads in that sample. Depending on how you define relative abundance, if the latter, it can be done in R with a .txt OTU table easily. 

Cheers,

Zoey

在 2013年6月13日星期四UTC-7上午11时13分31秒，EricG写道：

[Eric JC Galvez]

Thank you for your clarification, 

Best

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[Luis Peña]

Useful question :)