plotSummaryProfile           package:aCGH           R Documentation

_p_l_o_t_S_u_m_m_a_r_y_P_r_o_f_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function display the genomic events and tests for the
     differences between groups if they are specified.

_U_s_a_g_e:

     plotSummaryProfile(aCGH.obj,
                        response = as.factor(rep("All", ncol(aCGH.obj))),
                        titles = unique(response[!is.na(response)]),
                        X = TRUE, Y = FALSE, maxChrom = 23,
                        chrominfo = human.chrom.info.Jul03,
                        num.plots.per.page = length(titles),
                        factor = 2.5, posThres=100, negThres=-0.75)

_A_r_g_u_m_e_n_t_s:

aCGH.obj: an object of aCGH class.

response: phenotype to compare. defaults to all the samples being
          analyzed together. 

  titles: titles for the groups, defaults to the name of the 'response' 

       X: logical indicating whether X needs to be shown 

       Y: logical indicating whether Y needs to be shown 

maxChrom: this parameter controls how many chromosomes will be plotted,
          from 1 to maxChrom

chrominfo: a chromosomal information associated with the mapping of the
          data 

num.plots.per.page: number of frequency plots per page. Default is the
          number of groups 

  factor: 'factor' specifies the number by which experimental
          variability should be multiples. Used only when tumor
          specific variability in 'aCGH.obj' is not NULL. Defaults to
          2.5

posThres: Threshold for gain. Set very high for homozygous deletion

negThres: Threshold for homozygous deletion

_D_e_t_a_i_l_s:

     This function utilizes output of the 'find.genomic.events' by
     plotting it and testing between groups. The test are performed
     using kruskal-wallis rank test.

_S_e_e _A_l_s_o:

     'aCGH' 'find.genomic.events'

_E_x_a_m_p_l_e_s:

     data(colorectal)

     ## Plotting summary of the sample profiles
     plotSummaryProfile(colorectal)

