format2lefse: Format otutab, metadata and taxonomy into LEfSe format

View source: R/format2lefse.R

format2lefseR Documentation

Format otutab, metadata and taxonomy into LEfSe format

Description

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

Usage

format2lefse(
  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 metagenome@126.com

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.