read_biom_v2: Read QIIME 2 data

In bramstone/qSIP: Quantitative stable isotope probing for microbial ecology

Read QIIME 2 data

Description

Reads BIOM V2 files created from QIIME 2 which utilize the HDF5 data format

Usage

read_biom_v2(file, list = F)

Arguments

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, getwd(). Tilde-expansion is performed where supported. This can be a compressed file (see connections).
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.

Details

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).

Value

read_qiime2_table returns a long-form data frame of microbial features (ASVs or OTUs) and sample IDs.

References

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.

See Also

read_qiime2_tax

Examples

data(example_data)

dat <- read_qiime2_table(data_name)
head(dat)

bramstone/qSIP documentation built on Nov. 22, 2023, 9:11 p.m.