Yiwen (Eva) Wang authored on 13/11/2023 09:09:46
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\alias{AD_data}
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\title{Anaerobic digestion study}
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\format{
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-A list containing three sub-lists of data \code{FullData},
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-\code{EgData} and \code{CorrectData}:
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+A list containing three TreeSummarizedExperiment objects |
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+\code{FullData}, \code{EgData} and \code{CorrectData}:
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\describe{
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-\item{FullData}{A list containing three data sets: \code{X.count}
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-which are the raw data represented as a matrix with 75 samples and 567 OTUs; |
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-\code{metadata} which is a data frame containing the meta data information
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-of samples in \code{X.count}; \code{taxa} which is a data frame containing
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-the taxonomy of each OTU in \code{X.count}.}
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-\item{EgData}{A list containing three data sets: \code{X.clr} which are the
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-filtered and centered log ratio transformed data including 75 samples and |
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-231 OTUs from the raw data in the \code{FullData} list; \code{Y.trt} which
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-is a factor of phenol concentrations for each sample that is the effect of |
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-interest in the AD study; \code{Y.bat} which is a factor of sample
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-processing dates for each sample treated as the batch effect.} |
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-\item{CorrectData}{A list containing seven data sets before or after batch
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-effect correction using different methods. Each data set includes 75 samples |
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-and 231 OTUs.}} |
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+\item{FullData}{A TreeSummarizedExperiment object containing the counts of 75
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+samples and 567 OTUs. The meta data information of each sample is stored in |
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+the rowData, while the taxonomy of each OTU is stored in the colData.} |
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+\item{EgData}{A TreeSummarizedExperiment object containing the values of 75
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+samples and 231 OTUs filtered and centered log ratio transformed from the |
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+\code{FullData} with raw counts.The rowData includes \code{Y.trt} and
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+\code{Y.bat}. \code{Y.trt} is the effect of interest, which is a factor of
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+phenol concentrations for each sample in the AD study; \code{Y.bat} is the
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+batch effect, which is a factor of sample processing dates for each sample. |
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+The taxonomy of each OTU is stored in the colData. The rowTree is built based |
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+on the \code{Y.bat}.}
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+\item{CorrectData}{A TreeSummarizedExperiment object containing seven
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+datasets before or after batch effect correction using different methods. |
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+Each assay includes 75 samples and 231 OTUs.}} |
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} |
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\source{
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The raw data were provided by Dr. Olivier Chapleur and published at |
Yiwen (Eva) Wang authored on 03/04/2023 08:52:34
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new file mode 100644 |
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/data-AD_data.r |
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+\docType{data}
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+\name{AD_data}
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+\alias{AD_data}
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+\title{Anaerobic digestion study}
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+\format{
|
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+A list containing three sub-lists of data \code{FullData},
|
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+\code{EgData} and \code{CorrectData}:
|
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+\describe{
|
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+\item{FullData}{A list containing three data sets: \code{X.count}
|
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+which are the raw data represented as a matrix with 75 samples and 567 OTUs; |
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+\code{metadata} which is a data frame containing the meta data information
|
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+of samples in \code{X.count}; \code{taxa} which is a data frame containing
|
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+the taxonomy of each OTU in \code{X.count}.}
|
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+\item{EgData}{A list containing three data sets: \code{X.clr} which are the
|
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+filtered and centered log ratio transformed data including 75 samples and |
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+231 OTUs from the raw data in the \code{FullData} list; \code{Y.trt} which
|
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+is a factor of phenol concentrations for each sample that is the effect of |
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+interest in the AD study; \code{Y.bat} which is a factor of sample
|
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+processing dates for each sample treated as the batch effect.} |
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+\item{CorrectData}{A list containing seven data sets before or after batch
|
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+effect correction using different methods. Each data set includes 75 samples |
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+and 231 OTUs.}} |
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+} |
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+\source{
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+The raw data were provided by Dr. Olivier Chapleur and published at |
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+the referenced article. Filtering and normalisation described in our package |
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+vignette. |
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+} |
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+\usage{
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+data('AD_data')
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+} |
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+\value{
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+None. |
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+} |
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+\description{
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+This study explored the microbial indicators that could improve the efficacy |
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+of anaerobic digestion (AD) bioprocess and prevent its failure. The samples |
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+were treated with two different ranges of phenol concentration (effect of |
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+interest) and processed at five different dates (batch effect). This study |
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+includes a clear and strong batch effect with an approx. balanced |
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+batch x treatment design. |
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+} |
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+\references{
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+\insertRef{chapleur2016increasing}{PLSDAbatch}
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+} |
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+\keyword{datasets}
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