phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
I am working with 16s data and have been provided a biome file and relative abundance tvs file, and I have the sample mapping file. When I attempted to load the Biom fill in r using import_biom, this resulted in many lines of "Warning: Empty taxonomy vector encountered." followed buy 'Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent".
I understand that this means my biom table is missing the taxonomy information. Previously the biom files I have worked with had OTU, Taxonomy, and tree information. I now realize that this biome file (I can provide the link if useful) is just the feature table. Any solutions to similar problems I have found involve regeneration the biom file in QIIME to include this information. However, these files were provided to me from a third party and I did not generate them.
I am trying to analyze my data in phyloseq with the information I have but not sure if this is possible or if I need to acquire additional files. It is also possible that I do not fully understand the feature table and I am misinterpreting the error I am receiving. I was thinking that with a OTU table, taxonomy table, and meta data I could at least generate generate relative abundance, alpha, and beta diversity.
I am working with 16s data and have been provided a biome file and relative abundance tvs file, and I have the sample mapping file. When I attempted to load the Biom fill in r using import_biom, this resulted in many lines of "Warning: Empty taxonomy vector encountered." followed buy 'Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent".
I understand that this means my biom table is missing the taxonomy information. Previously the biom files I have worked with had OTU, Taxonomy, and tree information. I now realize that this biome file (I can provide the link if useful) is just the feature table. Any solutions to similar problems I have found involve regeneration the biom file in QIIME to include this information. However, these files were provided to me from a third party and I did not generate them.
I am trying to analyze my data in phyloseq with the information I have but not sure if this is possible or if I need to acquire additional files. It is also possible that I do not fully understand the feature table and I am misinterpreting the error I am receiving. I was thinking that with a OTU table, taxonomy table, and meta data I could at least generate generate relative abundance, alpha, and beta diversity.