computeRunningMedians         package:Ringo         R Documentation

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

     Function to compute running medians (or other quantiles) on a
     tiling expression set.

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

     computeRunningMedians(xSet, probeAnno, modColumn = "Cy5",
     allChr = c(1:19, "X", "Y"), winHalfSize = 400, min.probes = 5,
     quant = 0.5, combineReplicates = FALSE, verbose = TRUE)

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

    xSet: Object of class 'ExpressionSet' holding the normalized probe
          intensity data

probeAnno: Environment holding the genomic positions of probes in the
          ExpressionSet

modColumn: Column of the ExpressionSet's 'phenoData' holding the
          samples' difference of interest

  allChr: Character vector of all chromosomes in genome

winHalfSize: Half the size of the window centered at a probe position,
          in which all other probes contribute to the calculation of
          the median.

min.probes: integer; if less probes are in the sliding window, NA
          instead of the median is returned. This meant to avoid to
          computing non-meaningful medians. If unwanted, set this to 1
          or less

   quant: numeric; which quantile to use for the smoothing. The default
          '0.5' means compute the median over the values in the sliding
          window.

combineReplicates: logical; should the median not be computed over
          individual samples in the ExpressionSet, but should samples
          be combined according to the column 'modColumn' of the
          'phenoData'. The median is then computed across all probe
          levels and samples of the same type in the window. The
          resulting ExpressionSet has so many columns as are there
          different entries in the column 'modColumn'

 verbose: logical; detailed progress output to STDOUT?

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

     An object of class 'ExpressionSet', holding smoothed intensity
     values for the probes of the supplied ExpressionSet. The number of
     results samples is the number of levels in the supplied
     'modColumn' of the supplied ExpressionSet's phenoData.

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

     Joern Toedling toedling@ebi.ac.uk

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

     'ExpressionSet', 'sliding.quantile'

_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 = c("9"), winHalfSize = 400, verbose = TRUE)
       if (interactive()){
        par(mfrow=c(1,1))
        chipAlongChrom(exampleX, chrom="9", xlim=c(34318000,34321000), ylim=c(-2,4), probeAnno=exProbeAnno, gff=exGFF)
        chipAlongChrom(smoothX, chrom="9", xlim=c(34318000,34321000),
     probeAnno=exProbeAnno, itype="l", ilwd=4, paletteName="Spectral",
     add=TRUE)
       }

