R/ChIPpeakAnno-deprecated.R

In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

#' Deprecated Functions in Package ChIPpeakAnno
#' 
#' These functions are provided for compatibility with older versions of R
#' only, and may be defunct as soon as the next release.
#' 
#' findOverlappingPeaks is now deprecated wrappers for
#' \code{\link{findOverlapsOfPeaks}}
#' @rdname ChIPpeakAnno-deprecated
#' @param Peaks1 GRanges: See example below.
#' @param Peaks2 GRanges: See example below.
#' @param maxgap,minoverlap Used in the internal call to \code{findOverlaps()}
#' to detect overlaps. See
#' \code{?\link[IRanges:findOverlaps-methods]{findOverlaps}} in the
#' \pkg{IRanges} package for a description of these arguments.
#' @param multiple TRUE or FALSE: TRUE may return multiple overlapping peaks in
#' Peaks2 for one peak in Peaks1; FALSE will return at most one overlapping
#' peaks in Peaks2 for one peak in Peaks1. This parameter is kept for backward
#' compatibility, please use select.
#' @param NameOfPeaks1 Name of the Peaks1, used for generating column name.
#' @param NameOfPeaks2 Name of the Peaks2, used for generating column name.
#' @param select all may return multiple overlapping peaks, first will return
#' the first overlapping peak, last will return the last overlapping peak and
#' arbitrary will return one of the overlapping peaks.
#' @param annotate Include overlapFeature and shortestDistance in the
#' OverlappingPeaks or not.  1 means yes and 0 means no. Default to 0.
#' @param ignore.strand When set to TRUE, the strand information is ignored in
#' the overlap calculations.
#' @param connectedPeaks If multiple peaks involved in overlapping in several
#' groups, set it to "merge" will count it as only 1, while set it to "min"
#' will count it as the minimal involved peaks in any concered groups
#' @param \dots Objects of \link[GenomicRanges:GRanges-class]{GRanges}: See
#' also \code{\link{findOverlapsOfPeaks}}.
#' @seealso \code{\link{Deprecated}}, \link{findOverlapsOfPeaks},
#' \link{toGRanges}
#' @name ChIPpeakAnno-deprecated
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