read_biom_v2 | R Documentation |
Reads BIOM V2 files created from QIIME 2 which utilize the HDF5 data format
read_biom_v2(file, list = F)
file |
The name of the file which the feature data are to be read from. Each row of the table appears as one line of the file.
If it does not contain an absolute path, the file name is relative to the current working directory, This can be a compressed file (see |
list |
Whether or not to return the structure of the HDF5 file. If TRUE, returns only the list of the file contents. If FALSE (the default), returns the actual BIOM data. |
QIIME 2 uses the term features to refer to microbial taxonomic units in a way that is agnostic to the user's decision to use ASVs or OTUs. OTUs must first be clustered in QIIME 2, commonly at 97% sequence similarity. ASVs represent unique sequences and so these tables will be larger than OTU tables for the same data set. QIIME 2 favors ASVs by default. For a discussion on the benefits of using ASVs over OTUs see: https://www.nature.com/articles/ismej2017119 (referenced below).
read_qiime2_table
returns a long-form data frame of microbial features (ASVs or OTUs) and sample IDs.
Callahan, B.J., P.J. McMurdie, S.P. Holmes. 2017. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME Journal 11: 2639-2643.
read_qiime2_tax
data(example_data)
dat <- read_qiime2_table(data_name)
head(dat)
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