importing BIOM file · Issue #443 · joey711/phyloseq (original) (raw)

Hi Joey711,

I have been trying to import a biom file that I generated with qiime, the file is binary file, it seems that is new format for this kind of files, then when trying to work with it in R I get this error:

This is my code so far:

#Importing with BIOM function
biom_file <- "./COI_seed_otu_table.biom"
tree_file <- "./COI_fasttree_usearch.tre"

COI_data <- import_biom(biom_file)

COI_data <- import_biom(biom_file)
Error in nchar(content) : invalid multibyte string 1

#importing with qiime function
COI_data <- import_qiime(biom_file)

COI_data <- import_qiime(BIOMfilename = biom_file)
Error in arglist[sapply(arglist, is.component.class)] :
invalid subscript type 'list'

Maybe I am missing something or should I use an older version of BIOM file?