Update MAG-related documentation (#32)

EBI-Metagenomics · Sep 30, 2024 · 93728e3 · 93728e3
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diff --git a/R/getData.R b/R/getData.R
@@ -62,8 +62,17 @@
 #' res <- getData(
 #'     type = "genomes", accession.type = "genome-catalogues",
 #'     accession = catalogues[1, "id"], max.hits = 100)
+#' # See the data.
 #' head(res)
-#'
+#' # It includes for instance summary of the CAZy
+#' # (Carbohydrate-Active enZymes) annotations as a counts per category
+#' cazy <- res[ , grepl("annotations.cazy", colnames(res)), drop = FALSE]
+#' head(cazy)
+#' # Moreover, it includes a sample list. This sample list represents a 
+#' # collection of samples where the MAG was identified. Thr data has also the
+#' # completeness of MAG in a sample.
+#' head(res[ c("metadata.Sample_accession", "metadata.Completeness")])
+#' 
 #' @seealso
 #' \code{\link[HoloFoodR:getResult]{getResult}}
 #'

diff --git a/man/getData.Rd b/man/getData.Rd