combineRIP {RIPSeeker} | R Documentation

## Combined predictions from (presumably) biological replicates.

### Description

A simple helper function that combines multiple prediction lists from biological replicates into a single list.

### Usage

    combineRIP(ripPath, pattern="gff3$",
    	combineOption="intersect",
    	pvalCutoff=1, pvalAdjCutoff=1, eFDRCutoff=1,
    	logOddCutoff=-Inf, maxgap=1e3, minIntersect, genomeBuild)

### Arguments

`ripPath` | Path to predictions list in a select format as indicated by the file extension.
`pattern` | Pattern for the names of the prediction files to combine. The file names are expected to have a common extension such as "bed", "gff3", "gtf", but this is not enforced. Default: "gff3$" (i.e. the default output RIPregions.gff3 from `ripSeek`).
`combineOption` | Options on how to combine the peaks including: `"intersect"`: is selected (default), only peaks in each biological replicate list that overlap with or are adjacent within `maxgap` nucleotides to at least `minIntersect` other replicates will be kept. If `minIntersect` is unspecified, then only the peaks that consistently predicted in all replicates are kept. `"merge"`: All overlapping peaks from the replicates will be merged into one peak. `"union"`: All overlapping peaks from the replicates will be merged into one peak.
`pvalCutoff` | Threshold for the p-value cutoff. Only peaks with p-value less than the `logOddCutoff` will be reported. Default: 1 (i.e. no cutoff).
`pvalAdjCutoff` | Threshold for the adjusted p-value cutoff. Only peaks with adjusted p-value less than the `logOddCutoff` will be reported. Default: 1 (i.e. no cutoff).
`eFDRCutoff` | Threshold for the empirical false discovery rate (eFDR). Only peaks with eFDR less than the `eFDRCutoff` will be reported. Default: 1 (i.e. no cutoff).
`logOddCutoff` | Threshold for the log odd ratio of posterior for the RIP over the background states (See `seekRIP`). Only peaks with logOdd score greater than the `logOddCutoff` will be reported. Default: -Inf (i.e. no cutoff).
`maxgap` | Maximum gap allowed to determine two peaks agree with each other.
`minIntersect` | Mininum number of replicates required to have peaks either intersect or are adjacent to the peak in other replciate.
`genomeBuild` | Genome build used to obtain the chromosome information from online UCSC database to assign chromosome length to the `GRanges` object created as the combined peak list.

### Value

`gr` | `GRanges` object containning chromosome locations of the combined peaks.

### Note

Please run `ripSeek` first on all biological replicates and renamed each "RIPregions.gff3" output to correspond to different biological replicates and place all of the files into a single folder. The path of this folder can then be used as the input argument for `ripPath`.

### Author(s)

Yue Li

### References

P. Aboyoun, H. Pages and M. Lawrence. GenomicRanges: Representation and manipulation of genomic intervals. R package version 1.8.9.

Michael Lawrence, Vince Carey and Robert Gentleman. rtracklayer: R interface to genome browsers and their annotation tracks. R package version 1.16.3.

### See Also

`combineAlignGals, ripSeek, import, import, reduce, countOverlaps`

### Examples

    # Retrieve system files
    ripPath <- system.file("extdata/RIPregions", package="RIPSeeker")

    gr1 <- combineRIP(ripPath, combineOption="intersect", genomeBuild="mm9")

    gr2 <- combineRIP(ripPath, combineOption="merge", genomeBuild="mm9")

    gr3 <- combineRIP(ripPath, combineOption="union", genomeBuild="mm9")

    length(gr1)

    length(gr2)

    length(gr3)

[Package RIPSeeker version 1.20.0 Index]