Ringo (version 1.36.0)

findChersOnSmoothed: 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?

Value

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

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.

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)