plotStatistics        package:GeneRegionScan        R Documentation

_P_l_o_t _S_t_a_t_i_s_t_i_c_s

_D_e_s_c_r_i_p_t_i_o_n:

     Internal function that will assist plotOnGene in identifying
     probes that are significantly changed in comparison with a given
     pData column.

_U_s_a_g_e:

         plotStatistics(object, probeData, label, summaryType, testType, interval=NULL,
         forcePValue=FALSE, verbose=TRUE, positionVector, ylim, xlim, cutoff=0.2)

_A_r_g_u_m_e_n_t_s:

  object: A ProbeLevelSet object or a regular ExpressionSet object (in
          which case a probeData argument is required.

probeData: Optional if a ProbeLevelSet is submitted as object argument.
          Otherwise it must be a data frame with rownames corresponding
          to the featureNames of the ExpressionSet and a column named
          "sequence" with the probe sequences as character strings

   label: An optional character string specifying a column name in the
          pData of the object. If this argument is given, the gene plot
          will be colour coded based on the different groups (factors)
          in the pData entry. If a summaryType other than 'dots' is
          selected the summarisation is done stratified by the
          different groups in the pData.

summaryType: Character string specifying one of the following summary
          methods: 'median', 'mean', 'quartiles' or 'dots' (i.e. no
          summary). Specifies how all the sample values or all the
          samples values in a group if 'label' is given, should be
          summarised. Defaults to 'median'.

testType: Character string, defining a statistic procedure to identify
          especially interesting probes.

interval: Optional vector of two integers of bp positions. If given,
          the plot will only include the sequence from gene in the
          given interval. The x-axis annotation is preserved from
          original, so this is useful for zooming on specific regions.

forcePValue: Logical. Is used if the testType argument is used. If TRUE
          all significantly changed probes have P-value given on the
          plot. If FALSE, only plots with less than 10 probes
          significant write P-values. Plots can become very cluttered
          with data if set to TRUE

 verbose: TRUE or FALSE

positionVector: A vector of integers and names specifying the position
          along the x-axis of each probe.

    ylim: A vector of two integers. Specifies the decided ylim value
          passed into the plotting function.

    xlim: A vector of two integers. Specifies the decided xlim value
          passed into the plotting function.

  cutoff: Integer specifying at what p-value probes should be circled
          when using the 'testType' variable. Defaults to 0.2. For
          cutoffs higher than 0.05, all probes with P >0.05 will be
          circled in grey instead of black.

_D_e_t_a_i_l_s:

     This function is not meant to be called by the user. It acts as an
     adapter between plotOnGene and either doProbeLinear or
     doProbeTTest depending on the testType variable.

_V_a_l_u_e:

     No value, but decorates an existing plotOnGene plot with circles
     and p-values for all probes that are significant when
     investigating label with testType

_A_u_t_h_o_r(_s):

     Lasse Folkersen

_S_e_e _A_l_s_o:

     'doProbeLinear', 'doProbeTTest', 'plotOnGene'

