R/data_motifAnnotations.R

In aertslab/RcisTarget: RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

#' Documentation for the data

#' @rdname motifAnnotations
#' @name motifAnnotations
#' @aliases motifAnnotations_hgnc motifAnnotations_mgi motifAnnotations_dmel 
#' motifAnnotations_hgnc_v9 motifAnnotations_mgi_v9 motifAnnotations_dmel_v9
#' motifAnnotations_hgnc_v8 motifAnnotations_mgi_v8 motifAnnotations_dmel_v8
#' @title Annotations of Motifs to TFs
#' @description 
#' \itemize{
#' \item{\bold{motifAnnotations_hgnc}: }{Annotations to \bold{HUMAN} transcription factors for 
#'   the rankings using motif collection version 10.
#'   Source: \emph{motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl}}
#'  
#' \item{\bold{motifAnnotations_mgi}: }{Contains the annotations to \bold{MOUSE} transcription factors for 
#' the rankings using motif collection version 10.
#' Source: \emph{motifs-v10nr_clust-nr.mgi-m0.001-o0.0.tbl}}
#' 
#' \item{\bold{motifAnnotations_dmel}: }{Contains the annotations to \bold{FLY} transcription factors for 
#' the rankings using motif collection version 10.
#' Source: \emph{motifs-v10nr_clust-nr.flybase-m0.001-o0.0.tbl}}
#' }
#' \bold{Previous versions}: 
#' 
#' Annotations for motif collection version 9 ('mc9nr').
#' \itemize{
#'     \item{Human: motifAnnotations_hgnc_v9 (\emph{motifs-v9-nr.hgnc-m0.001-o0.0.tbl}})
#'     \item{Mouse: motifAnnotations_mgi_v9 (\emph{motifs-v9-nr.mgi-m0.001-o0.0.tbl}})
#'     \item{Fly: motifAnnotations_dmel_v9 (\emph{motifs-v9-nr.flybase-m0.001-o0.0.tbl}})
#'     }
#'     
#' Annotations for motif collection version 8 ('mc8nr'). 
#' - Deprecated: Will be removed in upcoming versions of the package
#' \itemize{
#'     \item{Fly: motifAnnotations_dmel_v8 (\emph{motifs-v8-nr.flybase-m0.001-o0.0.tbl}})
#'     }
#' 
#' 
#' These objects are meant to be provided to RcisTarget without modification, 
#' but it can also be explored by the user 
#' to obtain further information about the motifs.
#' The original files can be downloaded from \code{https://resources.aertslab.org/cistarget/motif2tf/}
#' Columns:
#' \itemize{
#'  \item{\bold{motif}: }{Motif ID.}
#'  \item{\bold{TF}: }{Transcription factor (or inferred gene).}
#'  \item{\bold{directAnnotation}, \bold{inferred_Orthology}, 
#'        \bold{inferred_MotifSimil}: }
#'     {Boolean values indicating whether the motif is 
#'        annotated to the TF in the source database ("directAnnotation"), 
#'        or whether it was inferred by orthology ("inferred_Orthology") 
#'        or motif similarity ("inferred_MotifSimil").}
#'  \item{\bold{Description}: }{Description of the source of the annotation.}
#'    \item{\bold{annotationSource}: }{
#'      Source of the annotation formatted as factor (e.g. for subsetting). 
#'      Levels: directAnnotation, inferredBy_Orthology, 
#'      inferredBy_MotifSimilarity, inferredBy_MotifSimilarity_n_Orthology.}
#' }
#' @docType data
#' @seealso importAnnotations, RcisTarget
#' @keywords datasets
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