R/data.R

In gclink: Gene-Cluster Discovery, Annotation and Visualization

#' BLASTP Results for test Proteins
#'
#' A dataset containing BLASTP alignment results for proteins from test genomes of bacteria,
#' including alignment metrics.
#'
#' @format A data frame with multiple rows and 12 variables:
#' \describe{
#'   \item{qaccver}{Character. Protein query identifier.}
#'   \item{saccver}{Character. Subject protein identifier from reference databases.}
#'   \item{pident}{Numeric. Percentage identity between query and subject sequences.}
#'   \item{length}{Numeric. Length of the aligned sequence region.}
#'   \item{mismatch}{Numeric. Number of mismatches in the alignment.}
#'   \item{gapopen}{Numeric. Number of gap openings in the alignment.}
#'   \item{qstart}{Numeric. Start position in query sequence.}
#'   \item{qend}{Numeric. End position in query sequence.}
#'   \item{sstart}{Numeric. Start position in subject sequence.}
#'   \item{send}{Numeric. End position in subject sequence.}
#'   \item{evalue}{Numeric. Expect value for the alignment.}
#'   \item{bitscore}{Numeric. Bit score for the alignment.}
#' }
#' @export
"blastp_df"

#' Photosynthesis Gene Classification Groups
#'
#' A dataset mapping photosynthesis-related genes to their functional groups and subunits.
#'
#' @format A data frame with multiple rows and 3 variables:
#' \describe{
#'   \item{gene}{Character. Gene identifier (e.g., "bchB").}
#'   \item{gene_group}{Character. Functional group (e.g., "bch").}
#'   \item{gene_label}{Character. Subunit designation (e.g., "B").}
#' }
#' @export
"PGC_group"

#' Photosynthesis Gene List
#'
#' A comprehensive list of genes involved in photosynthetic processes.
#'
#' @format A character vector containing gene identifiers:
#' \describe{
#'   Each element represents a photosynthesis-related gene symbol (e.g., "acsF", "bchB").
#' }
#' @export
"photosynthesis_gene_list"

#' Genomic Sequence Data with Annotations
#'
#' A dataset containing DNA sequences from test bacteria with detailed annotation metadata.
#' The first column combines multiple annotation elements separated by semicolons.
#'
#' @format A data frame with multiple rows and 2 variables:
#' \describe{
#'   \item{SeqName}{Character. Combined annotation fields separated by semicolons, containing:
#'     \itemize{
#'       \item \code{ID}: Sequence identifier (e.g., "1_7")
#'       \item \code{partial}: Completion status ("00" for complete, "01" for partial)
#'       \item \code{start_type}: Translation initiation codon (e.g., "GTG", "ATG")
#'       \item \code{rbs_motif}: Ribosome binding site motif (e.g., "GGAG/GAGG")
#'       \item \code{rbs_spacer}: RBS spacer length (e.g., "5-10bp")
#'       \item \code{gc_cont}: GC content (e.g., "0.673")
#'     }
#'   }
#'   \item{Sequence}{Character. DNA sequence (when available) in FASTA format}
#' }
#' @export
"seq_data"

#' EggNOG Functional Annotation Results
#'
#' A dataset containing EggNOG functional annotation results,
#' including taxonomic classification, functional categories, and domain information.
#'
#' @format A data frame with multiple rows and 21 variables:
#' \describe{
#'   \item{#query}{Character. Protein query identifier (e.g., "Houyiibacteriaceae--LLY-WYZ-15_3---k141_356661_13").}
#'   \item{seed_ortholog}{Character. Subject protein identifier from EggNOG database (e.g., "1168065.DOK_14784").}
#'   \item{evalue}{Numeric. Expect value for the annotation.}
#'   \item{score}{Numeric. Annotation bitscore.}
#'   \item{eggNOG_OGs}{Character.}
#'   \item{max_annot_lvl}{Character.}
#'   \item{COG_category}{Character.}
#'   \item{Description}{Character. Functional description (e.g., "Bacterial regulatory proteins, tetR family").}
#'   \item{Preferred_name}{Character. Gene name if available (e.g., "cobB").}
#'   \item{GOs}{Character.}
#'   \item{EC}{Character. Enzyme Commission number if applicable (e.g., "2.7.7.49").}
#'   \item{KEGG_ko}{Character. KEGG Orthology identifier if available (e.g., "ko:K00986").}
#'   \item{KEGG_Pathway}{Character.}
#'   \item{KEGG_Module}{Character.}
#'   \item{KEGG_Reaction}{Character.}
#'   \item{KEGG_rclass}{Character.}
#'   \item{BRITE}{Character.}
#'   \item{KEGG_TC}{Character.}
#'   \item{CAZy}{Character.}
#'   \item{BiGG_Reaction}{Character.}
#'   \item{PFAMs}{Character.}
#' }
#' @export
"eggnog_df"

#' KEGG Orthology (KO) Group Classification
#'
#' A dataset mapping KEGG Orthology (KO) identifiers to their functional groups and gene symbols.
#'
#' @format A data frame with multiple rows and 3 variables:
#' \describe{
#'   \item{gene}{Character. KEGG Orthology identifier (e.g., "K04035").}
#'   \item{gene_group}{Character. Functional group (e.g., "acsF").}
#'   \item{gene_label}{Character. Gene symbol (e.g., "acsF").}
#' }
#' @export
"KO_group"

.reference_gc_data <- function() {
  list(
    ref1 = blastp_df,
    ref2 = PGC_group,
    ref3 = photosynthesis_gene_list,
    ref4 = seq_data,
    ref5 = eggnog_df,
    ref6 = KO_group
  )
  invisible(NULL)
}