findChersOnSmoothed {Ringo} | R Documentation

## Find ChIP-enriched regions on smoothed ExpressionSet

### Description

Given an ExpressionSet of smoothed probe intensities, an environment with the mapping of probes to chromosomes, and a vector of thresholds for calling genomic sites enriched, this function finds the 'chers' (ChIP-enriched regions) consisting of enriched genomic positions, with probes mapped to them. 'Adjacent' enriched positions are condensed into a single Cher.

### Usage

    findChersOnSmoothed(smoothedX, probeAnno, thresholds, allChr = NULL,
       distCutOff = 600, minProbesInRow = 3, cellType = NULL,
       antibodyColumn=NULL, checkUnique = TRUE, uniqueCodes = c(0),
       verbose = TRUE)

### Arguments

`smoothedX` | Object of class `ExpressionSet` holding the smoothed probe intensities, e.g. the result of function `computeRunningMedians`.
`probeAnno` | environment containing the probe to genome mapping
`thresholds` | numeric vector of threshold above which smoothed probe intensities are considered to correspond to enriched probes. The vector has to be of length equal the number of samples in `smoothedX`, with a single threshold for each sample.
`allChr` | character vector of all chromosomes on which enriched regions are sought. Every chromosome here has to have probes mapped to it in the `probeAnno` environment. By default (`NULL`) the `chromosomeNames` of the probeAnno object are used.
`distCutOff` | integer; maximum amount of base pairs at which enriched probes are condensed into one Cher.
`minProbesInRow` | integer; minimum number of enriched probes required for a Cher; see `details` for further explanation.
`cellType` | character; name of cell type the data comes from, is either a. of length one indicating the column of `pData(smoothedX)` that holds the cell type OR b. of length one indicating the common cell type for all samples in the `ExpressionSet` OR c. of length equal to `ncol(smoothedX)` specifying the cell type of each sample individually.
`antibodyColumn` | the name or number of the column of the `pData(smoothedX)` that holds the description of the antibody used for each sample. This information is used to annotate found ChIP-enriched regions accordingly. If `NULL` (default), the `sampleNames` of `smoothedX` are used.
`checkUnique` | logical; indicates whether the uniqueness indicator of probe matches from the probeAnno environment should be used.
`uniqueCodes` | numeric; which numeric codes in the chromosome-wise match-uniqueness elements of the probeAnno environment indicate uniqueness?
`verbose` | logical; extended output to STDOUT?

### Details

Specifying a minimum number of probes for a Cher (argument `minProbesInRow`) guarantees that a Cher is supported by a reasonable number of measurements in probe-sparse regions. For example, if there's only one enriched probe within a certain genomic 1kb region and no other probes can been mapped to that region, this single probe does arguably not provide enough evidence for calling this genomic region enriched.

### Value

A list of class `cherList`, holding objects of class `cher` that were found on the supplied data.

### Author(s)

Joern Toedling

### See Also

`cherByThreshold`,`computeRunningMedians`, `relateChers`

### Examples

      exDir <- system.file("exData",package="Ringo")
      load(file.path(exDir,"exampleProbeAnno.rda"))
      load(file.path(exDir,"exampleX.rda"))
      smoothX <- computeRunningMedians(exampleX, probeAnno=exProbeAnno,
           modColumn = "Cy5", allChr = "9", winHalfSize = 400)
      chersX <- findChersOnSmoothed(smoothX, probeAnno=exProbeAnno,
           thresholds=0.45, allChr="9", distCutOff=600, cellType="human")
      if (interactive())
        plot(chersX[[1]], smoothX, probeAnno=exProbeAnno, gff=exGFF)
      chersX <- relateChers(chersX, exGFF)
      as.data.frame.cherList(chersX)

[Package Ringo version 1.56.0 Index]