R/data.R

In bjmt/universalmotif: Import, Modify, and Export Motifs with R

#' Example motif in `universalmotif` format.
#'
#' A simple DNA motif. To recreate this motif:
#' `create_motif("TATAWAW", nsites = numeric())`
#'
#' @format [universalmotif-class]
"examplemotif"

#' Another example motif in `universalmotif` format.
#'
#' A simple DNA motif with a non-empty `multifreq` slot.
#' To recreate to this motif:
#' `add_multifreq(examplemotif, DNAStringSet(rep(c("CAAAACC", "CTTTTCC"), 3)))`
#'
#' @format [universalmotif-class]
"examplemotif2"

#' JASPAR2018 CORE database scores
#'
#' For use with [compare_motifs()]. The precomputed scores allow for fast P-value estimation.
#' These scores were
#' generated using [make_DBscores()] with the JASPAR2018 CORE motif set.
#' The scores are organized in a `DataFrame`.
#' In this `DataFrame` is the location and scale
#' of scores resulting from a statistical
#' distribution using the the comparisons of JASPAR2018 CORE motifs with
#' randomized motifs of the specified
#' `subject` and `target` motif length. Created using [make_DBscores()] from
#' universalmotif v1.4.0. The parameters used can be seen via
#' `S4Vectors::metadata(JASPAR2018_CORE_DBSCORES)`.
#'
#' @format `DataFrame` with function args in the `metadata` slot.
"JASPAR2018_CORE_DBSCORES"

#' Arabidopsis promoters as a `DNAStringSet`.
#'
#' 50 Arabidopsis promoters, each 1000 bases long. See the
#' "Sequence manipulation and scanning"
#' vignette for an example workflow describing extracting promoter
#' sequences.
#'
#' @format \code{\link{DNAStringSet}}
"ArabidopsisPromoters"

#' Arabidopsis motif in `universalmotif` format.
#'
#' Arabidopsis motif trained from [`ArabidopsisPromoters`] using
#' MEME version 4. This motif was generated at the command line using
#' the following command: `meme promoters.fa -revcomp -nmotifs 3  -mod anr -dna`.
#'
#' @format [universalmotif-class]
"ArabidopsisMotif"

#' Polygon coordinates for plotting letters.
#'
#' `DataFrame` of polygon coordinates used by [view_motifs()] for plotting
#' letters. It was generated using the `createPolygons` function from the
#' `gglogo` package for the font Roboto Medium.
#'
#' @format [DataFrame-class]
"fontDFroboto"