R/data.R

In Alice-MacQueen/CDBNgenomics: Genomics Using the Cooperative Dry Bean Nursery Dataset

#' Best Linear Unbiased Predictors for 21 phenotypes from the CDBN panel.
#'
#' A dataset containing best linear unbiased predictors (BLUPs) for 21
#'     phenotypes from the Cooperative Dry Bean Nursery (CDBN) diversity panel
#'     of 347 genotypes of Phaseolus vulgaris, 327 of which were phenotyped.
#'     BLUPs were derived for CDBN phenotypes using rrBLUP, and conditioning on
#'     a kinship matrix, the location the phenotype came from, and the location
#'     by year combination that the phenotype came from.
#'     The variables are as follows:
#'
#' \itemize{
#'   \item Taxa. Taxa ID of the Phaseolus vulgaris CDBN panel.
#'   \item Seq_ID. The ID of the sequenced line in the CDBN panel.
#'   \item GHmode. Mode of the growth habit scored in the CDBN.
#'   \item CDBN_ID. ID of the CDBN entry
#'   \item Gene_pool. Whether the CDBN entry came from the Mesoamerican or Andean gene pool.
#'   \item Race. The race of the CDBN entry: Durango, Jalisco, Mesoamerican, or Nueva Granada.
#'   \item Market_class_ahm. Market class of the CDBN entry
#'   \item Det_scr. Whether or not the CDBN entry was determinate
#'   \item Earliest_Year_CDBN. The earliest year the entry was grown in the CDBN.
#'   \item BM. BLUPs for biomass in kg
#'   \item BR. BLUPs for whether or not the entry had a blackroot BCMV response
#'   \item CB. BLUPs for common bacterial blight damage score
#'   \item CM. BLUPs for BCMV (bean common mosaic virus) damage score
#'   \item CT. BLUPs for curly top virus presence/absence
#'   \item DF. BLUPs for days to flowering
#'   \item DM. BLUPs for days to maturity
#'   \item EV. BLUPs for early vigor score
#'   \item GH. BLUPs for growth habit, on a 1-3 scale
#'   \item HB. BLUPs for halo blight damage score
#'   \item HI. BLUPs for harvest index (%)
#'   \item LG. BLUPs for lodging score
#'   \item PH. BLUPs for plant height, in cm
#'   \item RR. BLUPs for root rot damage score
#'   \item RU. BLUPs for rust damage score
#'   \item SA. BLUPs for seed appearance score
#'   \item SF. BLUPs for the duration of seed fill, in days.
#'   \item SW. BLUPs for seed weight, in mg.
#'   \item SY. BLUPs for seed yield, in kg per ha.
#'   \item WM. BLUPs for white mold damage score
#'   \item ZN. BLUPs for zinc deficiency damage score
#' }
#'
#' @name BLUPs
#' @docType data
#' @author Alice MacQueen \email{alice.macqueen@@utexas.edu}
#' @references \url{data_blah.com}
#' @keywords data
#' @usage data(BLUPs)
#' @format A data frame with 327 rows and 31 variables
NULL

#' Metadata for 327 entries in the CDBN panel.
#'
#' A dataset containing the metadata associated with 327 entries from the
#'     Cooperative Dry Bean Nursery (CDBN) diversity panel of Phaseolus
#'     vulgaris, all of which were phenotyped.
#'     The variables are as follows:
#'
#' \itemize{
#'   \item Genotype. Name associated with the CDBN entry
#'   \item SY. Seed yield average associated with the CDBN entry
#'   \item Taxa. Taxa ID of the Phaseolus vulgaris CDBN panel.
#'   \item Seq_ID. The ID of the sequenced line in the CDBN panel.
#'   \item GHmode. Mode of the growth habit scored in the CDBN.
#'   \item Gene_pool. Whether the CDBN entry came from the Mesoamerican or Andean gene pool.
#'   \item Race. The race of the CDBN entry: Durango, Jalisco, Mesoamerican, or Nueva Granada.
#'   \item Market_class_ahm. Market class of the CDBN entry
#'   \item Det_scr. Whether or not the CDBN entry was determinate
#'   \item Earliest_Year_CDBN. The earliest year the entry was grown in the CDBN.
#' }
#'
#' @name metadata
#' @docType data
#' @author Alice MacQueen \email{alice.macqueen@@utexas.edu}
#' @references \url{data_blah.com}
#' @keywords data
#' @usage data(metadata)
#' @format A data frame with 327 rows and 10 variables
NULL

#' Annotation information
#'
#' A dataset containing the annotation information from v2.1 of the Phaseolus
#'     vulgaris genome. The variables are as follows:
#'
#' \itemize{
#'   \item pacId.
#'   \item locusName. Locus name in Phaseolus vulgaris.
#'   \item transcriptName.
#'   \item peptideName.
#'   \item Pfam.
#'   \item Panther.
#'   \item KOG.
#'   \item ec.
#'   \item KO.
#'   \item GO.
#'   \item Best.hit.arabi.name
#'   \item arabi.symbol.
#'   \item arabi.defline.
#'  }
#'
#' @name anno_info
#' @docType data
#' @author Alice MacQueen \email{alice.macqueen@@utexas.edu}
#' @references \url{data_blah.com}
#' @keywords data
#' @usage data(anno_info)
#' @format A data frame with 1236881 rows and 9 variables
NULL

#' Phaseolus vulgaris gene ontology information
#'
#' A dataset containing gene ontology  information from v2.1 of the Phaseolus
#'     vulgaris genome. The variables are as follows:
#'
#' \itemize{
#'   \item GENEID. Locus name in Phaseolus vulgaris.
#'   \item variant. Which transcriptomic variant is associated with this locus.
#'   \item GOCategories. GO Categories associated with this locus.
#'   \item GOInfo. Additional information about the gene ontology categories.
#'  }
#'
#' @name Pv_GO
#' @docType data
#' @author Alice MacQueen \email{alice.macqueen@@utexas.edu}
#' @references \url{data_blah.com}
#' @keywords data
#' @usage data(Pv_GO)
#' @format A data frame with 1236881 rows and 9 variables
NULL

#' Phaseolus vulgaris kegg information
#'
#' A dataset containing the annotation information from v2.1 of the Phaseolus
#'     vulgaris genome for KEGG categores (the Kyoto Encyclopedia of Genes and
#'     Genomes). The variables are as follows:
#'
#' \itemize{
#'   \item GENEID. Locus name in Phaseolus vulgaris.
#'   \item variant. Which transcriptomic variant is associated with this locus.
#'   \item KEGG. KEGG Categories associated with this locus.
#'   \item KEGGInfo. Additional information about the KEGG categories.
#'  }
#'
#' @name Pv_kegg
#' @docType data
#' @author Alice MacQueen \email{alice.macqueen@@utexas.edu}
#' @references \url{data_blah.com}
#' @keywords data
#' @usage data(Pv_kegg)
#' @format A data frame with 1236881 rows and 9 variables
NULL

#' Annotation genomic ranges for Phaseolus vulgaris
#'
#' A sqlite object containing the genomic ranges for v2.1 of the Phaseolus
#'     vulgaris genome. This object can be used with the AnnotationDbi package
#'     and the function 'loadDb'.
#'
#' @name txdb
#' @docType data
#' @author Alice MacQueen \email{alice.macqueen@@utexas.edu}
#' @references \url{data_blah.com}
#' @keywords data
#' @usage data(txdb)
#' @format A data frame with 1236881 rows and 9 variables
NULL

#' Oeco ggplot theme
#'
#' A list containing the oeco ggplot2 theme for use in cdbn_standard_gwas and
#'     mash_plot_ ... functions.
#'
#' @name theme_oeco
#' @docType data
#' @author Alice MacQueen \email{alice.macqueen@@utexas.edu}
#' @references \url{data_blah.com}
#' @keywords data
#' @usage data(theme_oeco)
#' @format A list containing ggplot2 specifications
NULL