read_qiime2_tax: Read QIIME 2 data

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

Read QIIME 2 data

Description

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

Usage

read_qiime2_tax(
  file,
  confidence = TRUE,
  feature_type = c("OTU", "ASV"),
  fill_na = TRUE
)

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).
feature_type	Single character indicating whether the table is composed of ASVs (amplicon sequence variants) or OTUs (operational taxonomic units). feature_type accepts only one argument.
fill_na	Logical value indicating whether or not to return unclassified taxonomic values as blank (fill_na=FALSE) or NA.

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 tab-separated TSV table is created using qiime tools export using a taxonomy qza file.

Value

read_qiime2_tax returns a character matrix of taxonomic assignments from Kingdom to Species, identified to each microbial taxa by the row names of the matrix.

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_table

Examples

data(example_data)

dat <- read_qiime2_tax(data_name, feature_type='otu', fill_na=TRUE)
head(dat)

dat <- read_qiime2_tax(data_name, feature_type='otu', fill_na=FALSE)
head(dat)

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