plotGainLoss             package:snapCGH             R Documentation

_f_r_e_q_u_e_n_c_y _p_l_o_t_s _a_n_d _s_i_g_n_i_f_i_c_a_n_c_e _a_n_a_l_y_s_i_s

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

     The main application of this function is to plot the frequency of
     changes.

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

     plotGainLoss(segList, resT = NULL, pheno = rep(1,
                      ncol(log2ratios(segList))), chrominfo =
                      chrominfo.Mb, X = TRUE, Y = FALSE, rsp.uniq =
                      unique(pheno), all = length(rsp.uniq) == 1 &&
                      is.null(resT), titles = if (all) "All Samples" else
                      rsp.uniq, cutplot = 0, thres = 0.25, factor = 2.5, ylm
                      = c(-1, 1), p.thres = c(0.01, 0.05, 0.1), numaut = 22,
                      onepage = TRUE, colored = TRUE)

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

 segList: Object of class 'SegList'

    resT: Data frame having the same structure as the result of
          applying 'mt.maxT' or 'mt.minP' functions from Bioconductor's
          'multtest' package for multiple testing. The result is a data
          frame including the following 4 components: 'index',
          'teststat', 'rawp' and 'adjp'. 

   pheno: phenotype to compare.

chrominfo: Chromosomal information. Defaults to 'chrominfo.Mb' 

       X: Include X chromosome? Defaults to yes.

       Y: Include Y chromosome? Defaults to no.

rsp.uniq: 'rsp.uniq' specified the codes for the groups of interest.
          Default is the unique levels of the phenotype. Not used when
          'all' is T. 

     all: 'all' specifies whether samples should be analyzed by
          subgroups (T) or together (F). 

  titles: 'titles' names of the groups to be used. Default is the
          unique levels of the 'pheno'. 

 cutplot: only clones with at least 'cutplot' frequency of gain and
          loss are plotted. 

   thres: 'thres' is either a vector providing unique threshold for
          each sample or a vector of the same length as number of
          samples (columns in 'data') providing sample-specific
          threshold. Used for plotting the gain/loss frequency data as
          well as for clone screening and for significance analysis
          when 'threshold' is TRUE.Defaults to 0.25 

  factor: 'factor' specifies the number by which experimental
          variability should be multiplied.  Defaults to 2.5

     ylm: 'ylm' vertical limits for the plot

 p.thres: 'p.thres' vector of p-value ciut-off to be plotted. computed
          conservatively as the threshold corresponding to a given
          adjusted p-value. 

  numaut: 'numaut' number of the autosomes

 onepage: 'onepage' whether all plots are to be plotted on one page or
          different pages. When more than 2 groups are compared, we
          recommend multiple pages. 

 colored: Is plotting in color or not? Default is TRUE.

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

