R/data.R

In NElnour/annotator3D: Classification of genome motifs or features to TADs

#' Matched Motifs that Regulate H5-K9 Methylation
#'
#' The data set is obtained by scanning murine PPMs provided by Ngo \emph{et al.} with FIMO against mm10 chromsome 18. The top 50 matches by \emph{q}=value were selected and organized into a dataframe.
#'
#' @format A dataframe with 50 rows and 10 variables:
#' \describe{
#'   \item{motif_id}{chromosome 18 fragments start coordinates}
#'   \item{motif_alt_id}{chromosome 18 fragments end coordinates}
#'   \item{sequence_name}{chromsome name at which the matches were found}
#'   \item{start}{start coordinates of the matched motif on chromsome 18}
#'   \item{stop}{end coordinate of the matched motif on chromosome 18}
#'   \item{strand}{Either "+" or "-" denoting the strand orientation of the match}
#'   \item{score}{Maximum likelihood score}
#'   \item{p.value}{The probability that the motif matchs to the chromsome region bounded by start and stop coordinates.}
#'   \item{q.value}{The \emph{p}-value corrected by Benjamini and Hochsberg false discvery rate for multiple testing}
#'   \item{matched_sequence}{Consensus sequence of matched motif}
#' }
#'
#' @references {
#' Ngo V, Chen Z, Zhang K, Whitaker J, Wang M, Wang W. (2019) Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse. \emph{PNAS} \strong{116}(9): 3668--3677.
#' }
#' @source \url{https://www.pnas.org/content/116/9/3668}
"matchedMotifs"

#' Predicted chromsome loops in A549's chromsome 18
#'
#' A subset 216-by-3 dataframe containing predicted and Peackahu-merged chromatin loops in chromsome 18 of A549 cells.
#' @format A dataframewith 216 rows and 3 columns:
#' \describe{
#'   \item{chr}{chromosome 18}
#'   \item{start}{chromatin loops' start coordinates}
#'   \item{stop}{chromatin loops' end coordinates}
#' }
#' @references {
#' Salameh TJ, Wang X, Song F, Zhang B, Wright SM, Khunsriraksakul C, Yue F. (2019) A supervised learning framework for chromatin loop detection in genome-wide contact maps. \emph{biorXiv}. doi: \url{https://doi.org/10.1101/739698}
#' }
#' @source \url{http://promoter.bx.psu.edu/hi-c/publications.html}
"A549ChromLoops"


#' A Classified Annotation Track of H3K9me3 predictor in mm10 chromosome 18 loops
#'
#' A sample clustered annotation track generated by the classifiedAnnotationTrack function.
#'
"antrack"

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