smoother {bumphunter} | R Documentation

## Smooth genomic profiles

### Description

Apply smoothing to values typically representing the difference between two populations across genomic regions.

### Usage

    smoother(y, x = NULL, cluster, weights = NULL, smoothFunction,
             verbose = TRUE, ...)

### Arguments

`y` | A vector or matrix of values to be smoothed. If a matrix, each column represents a sample.
`x` | The genomic location of the values in y
`cluster` | A vector indicating clusters of locations. A cluster is typically defined as a region that is small enough that it makes sense to smooth across neighbouring locations. Smoothing will only be applied within a cluster, not across locations from different clusters
`weights` | weights used by the smoother.
`smoothFunction` | A function to be used for smoothing the estimate of the genomic profile. Two functions are provided by the package: `loessByCluster` and `runmedByCluster`.
`verbose` | Boolean. Should progress be reported?
`...` | Further arguments to be passed to `smoothFunction`

### Details

This function is typically called by bumphunter prior to identifying candidate bump regions. Smoothing is carried out within regions defined by the `cluster` argument.

### Value

`fitted` | The smoothed data values
`smoothed` | A boolean vector indicating whether a given position was smoothed
`spans` | The span used by the loess smoother. One per cluster.
`clusterL` | The number of locations in each cluster.
`smoother` | The name of the smoother used

### Author(s)

Rafael A. Irizarry and Martin J. Aryee

### See Also

`loessByCluster`, `runmedByCluster`

### Examples

    dat <- dummyData()

    # Enable parallelization
    require(doParallel)
    registerDoParallel(cores = 2)

    ## loessByCluster
    smoothed <- smoother(y=dat$mat[,1], cluster=dat$cluster, smoothFunction=loessByCluster,
                           bpSpan = 1000, minNum=7, minInSpan=5, maxSpan=1)
    ## runmedByCluster
    smoothed <- smoother(y=dat$mat[,1], cluster=dat$cluster, smoothFunction=runmedByCluster,
                         k=5, endrule="constant")
    # cleanup, for Windows
    bumphunter:::foreachCleanup()

[Package bumphunter version 1.28.0 Index]