read_qiime2_table | R Documentation |
Reads TSV tables of microbial features exported from QIIME 2's biom
format
read_qiime2_table(file, quiet = FALSE)
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 |
quiet |
Whether or not to produce messages notifying the user about file loading progress. Recommended for large tables (larger than 300 Mb, uncompressed). |
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.
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.
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)
dim(dat)
dat[1:10,1:10]
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.