format2lefse2: Format otutab, metadata and taxonomy into LEfSe format with...

In microbiota/amplicon: Statistics and visualization for microbiome data

Format otutab, metadata and taxonomy into LEfSe format with level prefix p_

Description

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

Usage

format2lefse2(
  otutab,
  taxonomy,
  metadata,
  thre = 0.01,
  groupID = "Group",
  output = "LEfSe.txt"
)

Arguments

otutab	OTUID in row and normalized OTU table
taxonomy	Taxonomy include seven taxonomy level in tsv format
metadata	matrix or dataframe, including sampleID and groupID
thre	threshold of OTU abundance, especially for lefse create properly cladogram
groupID	column name for group ID.

Details

By default, written 2 file

Value

LEfSe input with or without taxonomy letter.

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 37, 676-684, doi:10.1038/s41587-019-0104-4 (2019). DOI: https://doi.org/10.1038/s41587-019-0104-4

See Also

format2stamp

Examples

# Set six parameters: three input files, and three parameters
format2lefse(otutab, taxonomy, metadata, thre = 0.01, groupID = "Group", output = "LEfSe.txt")

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