summarize.clones            package:aCGH            R Documentation

_E_x_t_r_a_c_t_i_n_g _s_u_m_m_a_r_y _i_n_f_o_r_m_a_t_i_o_n _f_o_r _a_l_l _c_l_o_n_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     'summarize.clones' function is the text equivalent of
     'plotFreqStat' function - it summarizes the frequencies of changes
     for each clone accross tumors and when available assigns
     statistics. The resulting table can be easily exported.

_U_s_a_g_e:

     summarize.clones(aCGH.obj, resT = NULL, pheno = rep(1, ncol(aCGH.obj)), rsp.uniq = unique(pheno), thres = 0.25, factor = 2.5, all = length(rsp.uniq) == 1 && is.null(resT), titles = if (all) "all" else rsp.uniq)

_A_r_g_u_m_e_n_t_s:

aCGH.obj: 'aCGH.obj' object here

    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'.Default is the unique levels of
          the phenotype. Not used when 'all' is TRUE.

   pheno: phenotype to compare

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 TRUE.

   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. If 'aCGH.obj' has non-null 'sd.samples', then
          threshold is automatically replaced by tumor-specific sd
          multiplied by 'factor'. Clone is considered to be gained if
          it is above the threshold and lost if it below negative
          threshold. Defaults to 0.25

  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

     all: 'all' specifies whether samples should be analyzed by
          subgroups   (TRUE) or together (FALSE)

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

_V_a_l_u_e:

     Returns matrix containg the following information for each clones:
     annotation (same as in 'clones.info'), number and proportion of
     samples where clone is present,gained and lost; and the same in
     each group if more than one group. Additionally, if significance
     comparison has been done, value of the statistic, unadjusted
     p-value and adjusted p-values are included for each clone.

_A_u_t_h_o_r(_s):

     Jane Fridlyand

_S_e_e _A_l_s_o:

     'plotFreqStat', 'aCGH'

_E_x_a_m_p_l_e_s:

     data(colorectal)
     summarize.clones(colorectal)

