% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/CreateCrcBiomeScreenObject.R
\name{CreateCrcBiomeScreenObject}
\alias{CreateCrcBiomeScreenObject}
\title{Create a CrcBiomeScreen S4 object for microbiome-based CRC analysis}
\usage{
CreateCrcBiomeScreenObject(
  AbsoluteAbundance = NULL,
  TaxaData = NULL,
  SampleData = NULL,
  RelativeAbundance = NULL
)
}
\arguments{
\item{AbsoluteAbundance}{A numeric matrix or data frame containing absolute abundance data.}

\item{TaxaData}{A data frame containing taxonomic information for each feature.}

\item{SampleData}{A data frame containing sample-level metadata.}

\item{RelativeAbundance}{A numeric matrix or data frame containing relative abundance data.}
}
\value{
A A \code{CrcBiomeScreen} object. object.
\itemize{
\item \code{AbsoluteAbundance}: Absolute abundance data.
\item \code{RelativeAbundance}: Relative abundance data.
\item \code{TaxaData}: Taxonomic annotations.
\item \code{SampleData}: Sample metadata.
\item \code{TaxaLevelData}: Optional genus-level summary data.
\item \code{NormalizedData}: Normalized data.
\item \code{OriginalNormalizedData}: Original normalized data.
\item \code{ValidationData}: Optional validation dataset.
\item \code{OutlierSamples}: Character vector of outlier sample names.
\item \code{ModelData}, \code{ModelResult}, \code{EvaluateResult},
\code{PredictResult}: Optional model results and evaluation outputs
}
}
\description{
Constructor for the \code{CrcBiomeScreen} S4 class.
This function creates a structured container for microbiome data,
including absolute and relative abundance matrices, taxonomic annotations,
and sample metadata. It ensures compatibility with downstream modelling
and evaluation functions within the CrcBiomeScreen package.
}
\details{
If only relative abundance data are supplied, absolute abundance is estimated
using the total number of reads in \code{SampleData$number_reads}.
}
\examples{
# Minimal example with tiny toy data (required for Bioconductor checks)

# Create toy abundance matrices
rel_abund <- data.frame(
  Sample1 = c(10, 20, 70),
  Sample2 = c(30, 30, 40)
)
rownames(rel_abund) <- c("TaxaA", "TaxaB", "TaxaC")

taxa_info <- data.frame(
  Taxa = rownames(rel_abund),
  stringsAsFactors = FALSE
)

sample_info <- data.frame(
  number_reads = c(10000, 12000),
  condition = c("control", "CRC"),
  row.names = c("Sample1", "Sample2"),
  stringsAsFactors = FALSE
)

# Create object
obj <- CreateCrcBiomeScreenObject(
  RelativeAbundance = rel_abund,
  TaxaData = taxa_info,
  SampleData = sample_info
)

}
\seealso{
A \code{CrcBiomeScreen} object.
}
