runGLAD               package:snapCGH               R Documentation

_R_e_s_u_l_t_s _o_f _s_e_g_m_e_n_t_i_n_g _a_n _a_C_G_H_L_i_s_t _d_a_t_a _o_b_j_e_c_t _u_s_i_n_g _t_h_e _G_L_A_D _l_i_b_r_a_r_y

_D_e_s_c_r_i_p_t_i_o_n:

     This function allows the detection of breakpoints in genomic
     profiles obtained by array CGH technology and affects a status
     (gain, normal or lost) to each clone.  It requires that the
     library 'GLAD' is loaded.

_U_s_a_g_e:

     runGLAD(input, smoothfunc="lawsglad", base=FALSE, sigma = NULL, bandwidth=10,
     round=2, lambdabreak=8, lambdacluster=8, lambdaclusterGen=40,
     type="tricubic", param=c(d=6), alpha=0.001, method="centroid",
     nmax=8, verbose=FALSE, ...)

_A_r_g_u_m_e_n_t_s:

   input: An object of class 'MAList' or 'SegList'

smoothfunc: Type of algorithm used to smooth 'LogRatio' by a piecewise
          constant function. Choose either 'lawsglad', 'aws' or 'laws'.

    base: If 'TRUE', the position of clone is the physical position
          onto the chromosome, otherwise the rank position is used.

   sigma: Value to be passed to either argument 'sigma2'    of' aws'
          function or 'shape' of 'laws'. If 'NULL', sigma is calculated
          from the data.

bandwidth: Set the maximal bandwidth 'hmax' in the 'aws' or  'laws'
          function. For example, if 'bandwidth=10' then the 'hmax'
          value is set to 10*X_N where X_N is the position of the last
          clone.

   round: The smoothing results are rounded or not depending on the
          'round' argument. The 'round' value is passed to the argument
          'digits' of the 'round' function.

lambdabreak: Penalty term (lambda') used during the  *Optimization of
          the number of breakpoints* step.

lambdacluster: Penalty term (lambda*) used during the *MSHR clustering
          by chromosome* step.

lambdaclusterGen: Penalty term (lambda*) used during the *HCSR
          clustering throughout the genome* step.

    type: Type of kernel function used in the penalty term during the
          *Optimization of the number of breakpoints* step, the *MSHR
          clustering by chromosome* step and the *HCSR clustering
          throughout the genome* step.

   param: Parameter of kernel used in the penalty term.

   alpha: Parameter for ?????.

  method: The agglomeration method to be used during the *MSHR
          clustering by chromosome* and the *HCSR clustering throughout
          the genome* clustering steps.

    nmax: Maximum number of clusters (N*max) allowed during the the
          *MSHR clustering by chromosome* and the *HCSR clustering
          throughout the genome* clustering steps.

 verbose: If 'TRUE' some information are printed

     ...: 

_D_e_t_a_i_l_s:

     For a detailed explanation of the GLAD algorithm please see the
     relevant section of the GLAD manual: 'glad'

_V_a_l_u_e:

     The function returns an object of class 'SegList'

_S_e_e _A_l_s_o:

     'glad' 'MAList' 'runHomHMM' 'runDNAcopy' 'SegList'

