setMethod(
f = "show",
signature="ExposomeSet",
definition = function(object) {
cat("Object of class 'ExposomeSet' (storageMode: ", storageMode(object), ")\n", sep="")
cat(" . exposures description:\n")
cat(" . categorical: ", sum(fData(object)$`.type` == "factor"), "\n")
cat(" . continuous: ", sum(fData(object)$`.type` == "numeric"), "\n")
cat(" . exposures transformation:\n")
cat(" . categorical:", sum(fData(object)$`.fct` != ""), "\n")
cat(" . transformed:", sum(fData(object)$`.trn` != ""), "\n")
cat(" . standardized:", sum(fData(object)$`.std` != ""), "\n")
cat(" . imputed:", sum(fData(object)$`.imp` != ""), "\n")
adim <- dim(object)
cat(" . assayData:", adim[[1]], "exposures", adim[[2]], "individuals\n")
cat(" . element names:", paste(assayDataElementNames(object), collapse=", "), "\n")
cat(" . exposures:", .wrpvec(rownames(assayData(object)[["exp"]])), "\n")
cat(" . individuals:", .wrpvec(colnames(assayData(object)[["exp"]])), "\n")
adim <- dim(phenoData(object))
phe <- phenoData(object)
cat(" . phenoData:", adim[[1]], "individuals", adim[[2]], "phenotypes\n")
cat(" . individuals:", .wrpvec(rownames(pData(phenoData(object)))), "\n")
cat(" . phenotypes:", .wrpvec(colnames(pData(phenoData(object)))), "\n")
adim <- dim(featureData(object))
fte <- featureData(object)
cat(" . featureData:", adim[[1]], "exposures", adim[[2]], "explanations\n")
cat(" . exposures:", .wrpvec(rownames(pData(featureData(object)))), "\n")
cat(" . descriptions:", .wrpvec(colnames(pData(featureData(object)))), "\n")
cat("experimentData: use 'experimentData(object)'\n")
pmids <- pubMedIds(object)
if (length(pmids) > 0 && all(pmids != "")) {
cat(" pubMedIds:", paste(pmids, sep=", "), "\n")
}
cat("Annotation:", annotation(object), "\n")
}
)
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