findChersOnSmoothed          package:Ringo          R Documentation

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_D_e_s_c_r_i_p_t_i_o_n:

     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.

_U_s_a_g_e:

     findChersOnSmoothed(smoothedX, probeAnno, thresholds, allChr = c(1:19,
      "X", "Y"), distCutOff = 600, minProbesInRow = 3, cellType = NULL,
      checkUnique = TRUE, uniqueCodes = c(0), verbose = TRUE)

_A_r_g_u_m_e_n_t_s:

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 Chers are to be
          found. Every chromosome here has to have probes mapped to it
          in the 'probeAnno' environment.

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.

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?

_D_e_t_a_i_l_s:

     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.

_V_a_l_u_e:

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

_A_u_t_h_o_r(_s):

     Joern Toedling toedling@ebi.ac.uk

_S_e_e _A_l_s_o:

     'cherByThreshold','computeRunningMedians', 'relateChers'

_E_x_a_m_p_l_e_s:

       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)

