plotSegmentationSummary       package:snapCGH       R Documentation

_p_l_o_t_S_e_g_m_e_n_t_a_t_i_o_n_S_u_m_m_a_r_y

_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:

     plotSegmentationSummary(input, geList, response = as.factor(rep("All",
                      ncol(input))), titles =
                      unique(response[!is.na(response)]), X = TRUE, Y =
                      FALSE, maxChrom = 23, chrominfo = chrominfo.Mb,
                      num.plots.per.page = length(titles), factor = 2.5,
                      thresAbs = 100)

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

   input: an object of either 'SegList' or 'MAList' class

  geList: an object of 'GEList' 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 'SegList' is not NULL. Defaults to
          2.5

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

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

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

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

     'MAList' 'findGenomicEvents'

