#----------------------------------------------------------------------------------------------------
#' @import methods
#' @import TrenaProject
#' @importFrom AnnotationDbi select
#' @import org.Hs.eg.db
#'
#' @title TrenaProjectMouseMacrophage-class
#'
#' @name TrenaProjectMouseMacrophage-class
#' @rdname TrenaProjectMouseMacrophage-class
#' @aliases TrenaProjectMouseMacrophage
#' @exportClass TrenaProjectMouseMacrophage
#'
.TrenaProjectMouseMacrophage <- setClass("TrenaProjectMouseMacrophage",
contains="TrenaProject")
#----------------------------------------------------------------------------------------------------
#' Define an object of class TrenaProjectMouseMacrophage
#'
#' @description
#' Expression, variant and covariate data for the genes of interest (perhaps unbounded) for pre-term birth studies
#'
#' @rdname TrenaProjectMouseMacrophage-class
#'
#' @export
#'
#' @return An object of the TrenaProjectMouseMacrophage class
#'
TrenaProjectMouseMacrophage <- function(quiet=TRUE)
{
genomeName <- "mm10"
directory <- system.file(package="TrenaProjectMouseMacrophage", "extdata", "geneSets")
geneSet.files <- list.files(directory)
geneSets <- list()
for(file in geneSet.files){
full.path <- file.path(directory, file)
genes <- scan(full.path, sep="\t", what=character(0), quiet=TRUE)
geneSet.name <- sub(".txt", "", file)
geneSets[[geneSet.name]] <- genes
}
footprintDatabaseNames <- NA_character_;
expressionDirectory <- system.file(package="TrenaProjectMouseMacrophage", "extdata", "expression")
variantsDirectory <- system.file(package="TrenaProjectMouseMacrophage", "extdata", "variants")
footprintDatabaseHost <- NA_character_;
covariatesFile <- NA_character_;
stopifnot(file.exists(expressionDirectory))
#stopifnot(file.exists(variantsDirectory))
# stopifnot(file.exists(covariatesFile))
.TrenaProjectMouseMacrophage(TrenaProject(supportedGenes=geneSets[[1]],
genomeName=genomeName,
footprintDatabaseHost=footprintDatabaseHost,
footprintDatabaseNames=footprintDatabaseNames,
expressionDirectory=expressionDirectory,
variantsDirectory=variantsDirectory,
covariatesFile=covariatesFile,
quiet=quiet
))
} # TrenaProjectMouseMacrophage, the constructor
#----------------------------------------------------------------------------------------------------
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