Thank you guys!
I have found a way to do it, rank by rank ("Phylum", "Class", "Order"...)
according my dataset.
Here is the code I have used:
fungi_phyla = tax_glom(fungi, "Phylum") ## extract the taxonomic rank e.g.
Phylum
tax_table(fungi_phyla)
fungi_phyla_ab = transform_sample_counts(fungi_phy
The tax_table accessor function will give you the taxonomic ranks in a
table according to this website:
https://web.stanford.edu/class/bios221/labs/phyloseq/lab_phyloseq.html
otu_table will give you the data matrix with OTUs as *rows*. So you need
to transpose or adjust the code I suggested before
Hello,
thank you for the replies. My dataset is something like this:
> datafungi
BR1 BR2 BR3 BR4 BR5 F1 F2 F3 F4 F5 R1 R2 R3
R4 R5 W1 W2 W3 W4 W5
OTU_1 0.08 0.13 0.56 0.90 0.91 0.36 0.05 0.02 0.13 0.11 0.00 0.00 0.15
0.06 0.00 0.12 0.00 0.00 0.03 0.05
OTU
Gian,
Once you have your samples by OTU matrix row standardized, you can use a
level of your hierarchy (a vector matching the columns) and the
groupSums(your-matrix, 2, your-groups) function in the mefa4 package to get
your relative abundances.
Cheers,
Peter
Gian Maria Niccolò Benucci ezt írta
On Thu, 25 Jun 2015, Gian Maria Niccolò Benucci wrote:
I am working on a fungal dataset with 151 OTUs distributed in 20 samples.
I have imported it as phyloseq object and as normal species matrix as well
to work with the vegan package. I am trying to find a way to get relative
abundances at diff
Hello everyone,
I am working on a fungal dataset with 151 OTUs distributed in 20 samples. I
have imported it as phyloseq object and as normal species matrix as well to
work with the vegan package.
I am trying to find a way to get relative abundances at different
hierarchical level goruping the abun
