R/RasperGade16S_data.R

In wu-lab-uva/RasperGade16S: Prediction of 16S rRNA GCN with RasperGade

#' Default reference tree for RasperGade16S
#'
#' A phylo-class object containing 6408 reference tips/genomes
#'
#' @format A phylo-class object with 6408 tips, binary and rooted:
#' \describe{
#'   \item{tip.label}{reference genome names, in NCBI RefSeq accession number}
#'   \item{edge.length}{phylogenetic distance between nodes, in substitutions/site}
#'   \item{edge}{parent node and descendant node of an edge}
#'   \item{Nnode}{the number of nodes}
#' }
#' @source \url{https://github.com/wu-lab-uva/16S-rRNA-GCN-Predcition}
"RasperGade16S.reftree"

#' Default reference GCN for RasperGade16S
#'
#' A named vector of 6408 elements
#'
#' @format A named numeric vector with 6408 elements:
#' \describe{
#'   \item{values}{16S rRNA GCN of reference genomes}
#'   \item{names}{reference genome names, in NCBI RefSeq accession number}
#' }
#' @source \url{https://github.com/wu-lab-uva/16S-rRNA-GCN-Predcition}
"RasperGade16S.refGCN"

#' Predicted SILVA 132 GCN (Bacteria only) by RasperGade16S
#'
#' A named vector of 592605 elements
#'
#' @format A named numeric vector with 592605 elements:
#' \describe{
#'   \item{values}{16S rRNA GCN of SILVA bacterial OTUs}
#'   \item{names}{reference genome names, in NCBI RefSeq accession number}
#' }
#' @source \url{https://github.com/wu-lab-uva/16S-rRNA-GCN-Predcition}
"RasperGade16S.SILVA.GCN"

#' GreenGene 13.8 16S rRNA gene mask for RasperGade16S
#'
#' A character vector of 1287 elements
#'
#' @format A character vector of 1287 elements; each element has 4938 characters:
#' \describe{
#'   \item{values}{16S rRNA gene sequence at each position}
#'   \item{seq_id}{the attribute that marks the identity of each 16S rRNA gene sequence}
#' }
#' @source \url{https://github.com/wu-lab-uva/16S-rRNA-GCN-Predcition}
"RasperGade16S.GG.13.8.mask.keys"

#' Default full reference data for RasperGade16S
#'
#' A named list of 8 elements
#'
#' @format A named list with 8 elements:
#' \describe{
#'   \item{phy}{scaled reference tree}
#'   \item{model}{evolution model for GCN prediction}
#'   \item{epsilon}{tip-specific epsilon term}
#'   \item{scale.branch}{scaling factor for each branch, indexed by the descendant node}
#'   \item{epsilon.branch}{branch-specific epsilon term}
#'   \item{dat}{reference GCN}
#'   \item{original}{unscaled reference tree}
#'   \item{FMR}{marginal ancestral states for quick prediction of GCN}
#' }
#' @source \url{https://github.com/wu-lab-uva/16S-rRNA-GCN-Predcition}
"RasperGade16S.refdata"