ChIPpeakAnno-deprecated {ChIPpeakAnno} | R Documentation

## 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.

### Usage

      findOverlappingPeaks(Peaks1, Peaks2, maxgap = -1L,
                        minoverlap=0L, multiple = c(TRUE, FALSE),
                        NameOfPeaks1 = "TF1", NameOfPeaks2 = "TF2",
                        select=c("all", "first","last","arbitrary"),
                        annotate = 0, ignore.strand=TRUE,
                        connectedPeaks=c("min", "merge"), ...)
      BED2RangedData(data.BED,header=FALSE, ...)
      GFF2RangedData(data.GFF,header=FALSE, ...)

### Arguments

`Peaks1` | RangedData: See example below.
`Peaks2` | RangedData: 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 or RangedData: See also `findOverlapsOfPeaks`. Or any parameter need to be passed into read.delim function for 2RangedData function.
`header` | TRUE or FALSE, default to FALSE, indicates whether data file has header
`data.BED` | BED format data frame or BED filename, please refer to http://genome.ucsc.edu/FAQ/FAQformat#format1 for details
`data.GFF` | GFF format data frame or GFF file name, please refer to http://genome.ucsc.edu/FAQ/FAQformat#format3 for details

### Details

findOverlappingPeaks is now deprecated wrappers for `findOverlapsOfPeaks`

### See Also

`Deprecated`, findOverlapsOfPeaks, toGRanges

[Package ChIPpeakAnno version 3.12.7 Index]