findCluster               package:GLAD               R Documentation

_C_l_u_s_t_e_r_i_n_g _o_f _g_e_n_o_m_i_c _r_e_g_i_o_n_s

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

     The function 'findCluster' allows the clustering of regions.

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

     findCluster.profileChr(profileChr, region="Region", genome=TRUE,
                            lambda=10, nmin=1, nmax=10, type="tricubic",
                            param=c(d=6), verbose=FALSE, ...)

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

profileChr: Object of class 'profileChr'.

  region: Label which indicated where outliers are detected.

  genome: If 'TRUE', the "MSHR clustering by chromosome" clustering
          step is run otherwise it is the "HCSR clustering throughout
          the genome" clustering step.

  lambda: Penalty lambda*.

    nmin: Minimal number of cluster to find.

    nmax: Maximal number of cluster to find.

    type: Type of kernel to use in the penalty term (this arguments is
          passed to the 'kernelpen' function).

   param: Parameters of the kernel (this arguments is passed to the
          'kernelpen' function).

 verbose: If 'TRUE' some information are printed

     ...: Risk alpha used in 'detectOutliers'.

_V_a_l_u_e:

     An object of class 'profileChr' with the following element added
     to the data.frame 'profileValues':

     either:

 ZoneChr: indicates the regions which belongs to the same HCSR (if
          'genome=FALSE').

 ZoneGen: indicates HCSR which belongs to the same cluster (if
          'genome=TRUE').

_A_u_t_h_o_r(_s):

     Philippe Hup, Philippe.Hupe@curie.fr.

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

     'glad', 'detectOutliers'

