smoothSnp              package:SNPchip              R Documentation

_A _s_i_m_p_l_e _n_o_n_p_a_r_a_m_e_t_r_i_c _s_m_o_o_t_h_e_r _f_o_r _g_e_n_o_t_y_p_e _a_n_d _c_o_p_y _n_u_m_b_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     A loess smoother for finding regions of reduced copy number and
     loss of heterozygosity.

_U_s_a_g_e:

     smoothSnp(object, ...)

_A_r_g_u_m_e_n_t_s:

  object: Object derived from 'AnnotatedSnpSet'

     ...: For additional arguments see details.

_D_e_t_a_i_l_s:

     Additional arguments include the chromosomes (character vector)
     and samples (numerical vector) to smooth.  Options for smoothing
     are set by specifying the span and the method.  See the SNPchip
     vignette.

     See the R package VanillaICE for a hidden Markov model for more
     formal inference regarding regions of LOH and copy number
     alterations.

_V_a_l_u_e:

     An object of the same class, e.g., 'AnnotatedSnpSet', where
     assayData elements copyNumber and calls are replaced by the
     smoothed values.

_A_u_t_h_o_r(_s):

     Robert Scharpf

_R_e_f_e_r_e_n_c_e_s:

     RS

