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

