format2stamp: Format otutab and taxonomy into each level for STAMP

In microbiota/amplicon: Statistics and visualization for microbiome data

Format otutab and taxonomy into each level for STAMP

Description

Input otutab, taxonomy, and manual set abundance threshold. dplyr merge taxonomy.

Usage

format2stamp(otutab, taxonomy, thre = 1e-04, prefix = "tax")

Arguments

otutab	raw or normalized OTU table
taxonomy	Taxonomy include seven taxonomy level in tsv format
thre	threshold of OTU relative abundance, default 1 read per Million
prefix	prefix for output files

Details

By default, written 8 files The files list as the following:

• 1-7: Kingdom to Species together include 7 levels

• 8: filtered OTUs

Value

nothing, all table 1-8 saving in output directory.

Author(s)

Contact: Yong-Xin Liu [e-mail]

References

Jingying Zhang, Yong-Xin Liu, et. al. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice Nature Biotechnology. (2019) 37, 676-684. DOI: https://doi.org/10.1038/s41587-019-0104-4

See Also

format2lefse

Examples

# Set 4 parameters: 2 input files, and 2 parameters
format2stamp(otutab, taxonomy, thre = 0.01,  prefix = "tax")

microbiota/amplicon documentation built on April 30, 2023, 1:48 p.m.