Hi, all!
I have generated a biom file in qiime 2, which I am trying to export to R, with the phyloseq package, yet without success. What I have tried is:
biom = system.file("extdata", "taxa_table.biom", package = "phyloseq")
tree = system.file("extdata", "tree.nwk", package = "phyloseq")
import_biom(biom, tree, parseFunction = parse_taxonomy_greengenes)
The following code, retrieves this error:
Error in read_biom(biom_file = BIOMfilename) :
Both attempts to read input file:
either as JSON (BIOM-v1) or HDF5 (BIOM-v2).
Check file path, file name, file itself, then try again.
Browsing in the web, I understood that perhaps there could be a problem in the file path. Nevertheless I am sure that the name and the location are correct, but I am not able to introduce these files in R.
Any help would be deeply appreciated!
Thanks in advance!
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