% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/SplitTaxas.R
\name{SplitTaxas}
\alias{SplitTaxas}
\title{Split and clean taxonomy strings}
\usage{
SplitTaxas(CrcBiomeScreenObject)
}
\arguments{
\item{CrcBiomeScreenObject}{A A \code{CrcBiomeScreen} object. object.}
}
\value{
A A \code{CrcBiomeScreen} object. with TaxaData.
}
\description{
This function automatically detects the taxonomy string format (e.g., MetaPhlAn, QIIME, SILVA, GTDB),
splits the string into standard taxonomic ranks (Kingdom to Species),
retains the original taxonomy string in a new column (\code{OriginalTaxa}),
and refines labels such as "uncultured" or "unclassified" by appending the parent rank.
}
\examples{
# Minimal toy object for SplitTaxas demonstration

# Example taxonomic strings with up to Genus level
toy_taxa <- data.frame(
    Taxa = c(
        "D_0__Bacteria;D_1__Firmicutes;D_2__Clostridia;D_3__Lachnospirales;
        D_4__Lachnospiraceae;D_5__Roseburia","D_0__Bacteria;D_1__Firmicutes;
        D_2__Bacilli;D_3__Lactobacillales;D_4__Lactobacillaceae;
        D_5__Lactobacillus"),
    stringsAsFactors = FALSE
)

# Minimal object containing only the TaxaData slot needed for splitting
toy_obj <- new(
    "CrcBiomeScreen",
    AbsoluteAbundance   = data.frame(),
    RelativeAbundance   = data.frame(),
    TaxaData            = toy_taxa,
    SampleData          = data.frame(),
    TaxaLevelData       = NULL,
    NormalizedData      = NULL,
    OriginalNormalizedData = NULL,
    ValidationData      = NULL,
    ModelData           = NULL,
    ModelResult         = NULL,
    EvaluateResult      = list(),
    PredictResult       = NULL
)

# Run taxonomic splitting
SplitTaxas(toy_obj)
}
