read_qiime2_table: Read QIIME 2 data

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

Read QIIME 2 data

Description

Reads TSV tables of microbial features exported from QIIME 2's biom format

Usage

read_qiime2_table(file, quiet = FALSE)

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).
quiet	Whether or not to produce messages notifying the user about file loading progress. Recommended for large tables (larger than 300 Mb, uncompressed).

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).

The input table is created using qiime tools export using a feature table qza to create a biom file followed by biom convert to produce a tab-delimited feature table. read_qiime2_table uses scan to read in the data in two parts, first the column headers, and then the rest of the data.

Value

read_qiime2_table returns an integer matrix of microbial features (ASVs or OTUs) along rows and samples along columns. Feature ID codes are stored as row names, and sample codes as column names.

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)

dim(dat)
dat[1:10,1:10]

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