% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/format2lefse.R
\name{format2lefse}
\alias{format2lefse}
\title{Format otutab, metadata and taxonomy into LEfSe format}
\usage{
format2lefse(
  otutab,
  taxonomy,
  metadata,
  thre = 0.01,
  groupID = "Group",
  output = "LEfSe.txt"
)
}
\arguments{
\item{otutab}{OTUID in row and normalized OTU table}

\item{taxonomy}{Taxonomy include seven taxonomy level in tsv format}

\item{metadata}{matrix or dataframe, including sampleID and groupID}

\item{thre}{threshold of OTU abundance, especially for lefse create properly cladogram}

\item{groupID}{column name for group ID.}
}
\value{
LEfSe input with or without taxonomy letter.
}
\description{
Input otutab, taxonomy and metadata, and manual set abundance threshold and metadata column names.
dplyr merge taxonomy.
}
\details{
By default, written 2 file
}
\examples{
# Set six parameters: three input files, and three parameters
format2lefse(otutab, taxonomy, metadata, thre = 0.01, groupID = "Group", output = "LEfSe.txt")
}
\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: \url{https://doi.org/10.1038/s41587-019-0104-4}
}
\seealso{
format2stamp
}
\author{
Contact: Yong-Xin Liu \email{metagenome@126.com}
}
