ChIPpeakAnno-deprecated: Deprecated Functions in Package ChIPpeakAnno

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

Deprecated Functions in Package ChIPpeakAnno

Description

These functions are provided for compatibility with older versions of R only, and may be defunct as soon as the next release.

Arguments

Peaks1	GRanges: See example below.
Peaks2	GRanges: See example below.
maxgap, minoverlap	Used in the internal call to findOverlaps() to detect overlaps. See ?findOverlaps in the IRanges package for a description of these arguments.
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.
NameOfPeaks1	Name of the Peaks1, used for generating column name.
NameOfPeaks2	Name of the Peaks2, used for generating column name.
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.
annotate	Include overlapFeature and shortestDistance in the OverlappingPeaks or not. 1 means yes and 0 means no. Default to 0.
ignore.strand	When set to TRUE, the strand information is ignored in the overlap calculations.
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
...	Objects of GRanges: See also findOverlapsOfPeaks.

Details

findOverlappingPeaks is now deprecated wrappers for findOverlapsOfPeaks

See Also

Deprecated, findOverlapsOfPeaks, toGRanges

jianhong/ChIPpeakAnno documentation built on Feb. 2, 2024, 3:26 p.m.