diff --git a/R/getData.R b/R/getData.R index 0c3e51b..00fdf7e 100644 --- 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 index 8e27ce7..4345273 100644 --- a/man/getData.Rd +++ b/man/getData.Rd @@ -79,7 +79,16 @@ head(catalogues) 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{