BioNERO: Biological Network Reconstruction Omnibus

#' Maize gene expression data from Shin et al., 2021.
#'
#' Filtered expression data in transcripts per million (TPM) from
#' Shin et al., 2021. Genes with TPM values <5 in more than 60% of the samples
#' were removed to reduce package size. The expression data and
#' associated sample metadata are stored in a SummarizedExperiment object.
#'
#' @name zma.se
#' @format An object of class \code{SummarizedExperiment}
#' @references Shin, J., Marx, H., Richards, A., Vaneechoutte, D., Jayaraman,
#' D., Maeda, J., ... & Roy, S. (2021). A network-based comparative framework
#' to study conservation and divergence of proteomes in plant
#' phylogenies. Nucleic Acids Research, 49(1), e3-e3.
#' @examples
#' data(zma.se)
#' @usage data(zma.se)
"zma.se"


#' Rice gene expression data from Shin et al., 2021.
#'
#' Filtered expression data in transcripts per million (TPM) from
#' Shin et al., 2021. Genes with TPM values <5 in more than 60% of the samples
#' were removed to reduce package size. The expression data and
#' associated sample metadata are stored in a SummarizedExperiment object.
#'
#' @name osa.se
#' @format An object of class \code{SummarizedExperiment}
#' @references Shin, J., Marx, H., Richards, A., Vaneechoutte, D., Jayaraman,
#' D., Maeda, J., ... & Roy, S. (2021). A network-based comparative framework
#' to study conservation and divergence of proteomes in plant
#' phylogenies. Nucleic Acids Research, 49(1), e3-e3.
#' @examples
#' data(osa.se)
#' @usage data(osa.se)
"osa.se"


#' Filtered maize gene expression data from Shin et al., 2021.
#'
#' Filtered expression data in transcripts per million (TPM) from
#' Shin et al., 2021. This is the same data set described in \code{zma.se},
#' but it only contains the top 500 genes with the highest variances.
#' This data set was created to be used in unit tests and examples.
#'
#' @name filt.se
#' @format An object of class \code{SummarizedExperiment}
#' @references
#' Shin, J., Marx, H., Richards, A., Vaneechoutte, D., Jayaraman, D., Maeda,
#' J., ... & Roy, S. (2021). A network-based comparative framework to study
#' conservation and divergence of proteomes in plant
#' phylogenies. Nucleic Acids Research, 49(1), e3-e3.
#' @examples
#' data(filt.se)
#' @usage data(filt.se)
"filt.se"


#' Maize Interpro annotation
#'
#' Interpro protein domain annotation retrieved from the
#' PLAZA Monocots 4.0 database.
#' Only genes included in \code{zma.se} are present in this subset.
#'
#' @name zma.interpro
#' @format A 2-column data frame containing gene IDs and their
#' associated Interpro annotations.
#' @references
#' Van Bel, M., Diels, T., Vancaester, E., Kreft, L., Botzki, A.,
#' Van de Peer, Y., ... & Vandepoele, K. (2018). PLAZA 4.0: an integrative
#' resource for functional, evolutionary and comparative plant
#' genomics. Nucleic acids research, 46(D1), D1190-D1196.
#' @examples
#' data(zma.interpro)
#' @usage data(zma.interpro)
"zma.interpro"


#' Maize transcription factors
#'
#' Transcription factors and their families were downloaded from PlantTFDB 4.0.
#'
#' @name zma.tfs
#' @format A data frame with gene IDs of TFs and their associated families.
#' @references
#' Jin, J., Tian, F., Yang, D. C., Meng, Y. Q., Kong, L., Luo, J., &
#' Gao, G. (2016). PlantTFDB 4.0: toward a central hub for transcription
#' factors and regulatory interactions in plants. Nucleic acids research, gkw982.
#' @examples
#' data(zma.tfs)
#' @usage data(zma.tfs)
"zma.tfs"


#' Orthogroups between maize and rice
#'
#' The orthogroups were downloaded from the PLAZA 4.0 Monocots database.
#'
#' @name og.zma.osa
#' @format A 3-column data frame with orthogroups, species IDs and gene IDs.
#' @references
#' Van Bel, M., Diels, T., Vancaester, E., Kreft, L., Botzki, A.,
#' Van de Peer, Y., ... & Vandepoele, K. (2018). PLAZA 4.0: an integrative
#' resource for functional, evolutionary and comparative plant
#' genomics. Nucleic acids research, 46(D1), D1190-D1196.
#'
#' @examples
#' data(og.zma.osa)
#' @usage data(og.zma.osa)
"og.zma.osa"