summarize.peaks {BayesPeak} | R Documentation

## Summarize Peaks

### Description

Summarize Peaks - Combine the potentially enriched bins found by BayesPeak into contiguous peaks, and associate each with a posterior probability. `summarise.peaks` is an alias for `summarize.peaks`

### Usage

    summarize.peaks(x, threshold = 0.5, method = c("lowerbound", "max"), exclude.jobs = NULL)
    summarise.peaks(x, threshold = 0.5, method = c("lowerbound", "max"), exclude.jobs = NULL)

### Arguments

`x` | Raw output from the function `bayespeak`.
`threshold` | Numeric vector. `threshold` must have length equal to either 1 or `nrow(x$QC)` (i.e. the number of jobs). If `threshold` is of length 1, then for each job, all bins with a posterior probability (PP) lower than `threshold` will be discarded before summarising. If `threshold` is of length `nrow(x$QC)`, then jobs are taken to have separate thresholds - in other words, bins in job i will be discarded if they have a PP less than threshold[i]. Note that this behaviour is irrespective of how many jobs are excluded (see the exclude.jobs argument below) - excluded jobs are still assigned a PP threshold, which is essentially ignored.
`method` | The method used to combine the posterior probabilities of multiple peaks. Current methods are: `lowerbound`: A lower bound is found for the posterior probability of the region containing a peak. In contiguous regions of moderately high probability, this method should report a fairer value than `method = max`. Suppose we have a set of n non-intersecting calls within our region, with posterior probabilities p_1 to p_n respectively of containing peaks. Then the probability of there being a peak in this region is at least 1 - (1-p_1)...(1-p_n). We maximise this over all possible sets of non-intersecting calls within the region. (Usually, this will simply be a choice between exclusively using the offset or the non-offset analyses.) `max`: Combined region has probability equal to the maximum posterior probability over all the peaks it contains.
`exclude.jobs` | A vector of integers, denoting jobs to be excluded from later analysis. Alternatively, a logical vector (to be passed through `which()`).

### Value

A RangedData object corresponding to the peaks called - each range has an associated PP (Posterior Probability) value.

### Author(s)

Jonathan Cairns

### See Also

`bayespeak`.

### Examples

    dir <- system.file("extdata", package="BayesPeak")
    treatment <- file.path(dir, "H3K4me3reduced.bed")
    input <- file.path(dir, "Inputreduced.bed")

    ##look at specific region 92-95Mb on chromosome 16
    ##(we've used half the number of iterations here to reduce the time this example takes)
    raw.output <- bayespeak(treatment, input, chr = "chr16", start = 9.2E7, end = 9.5E7, iterations = 5000L, use.multicore = TRUE)
    output <- summarize.peaks(raw.output)
    output

    ##higher threshold
    output.ht <- summarize.peaks(raw.output, threshold = 0.9)
    output.ht

[Package BayesPeak version 1.38.0 Index]