calculateCnSE           package:VanillaICE           R Documentation

_C_a_l_c_u_l_a_t_e_s _c_o_p_y _n_u_m_b_e_r _s_t_a_n_d_a_r_d _e_r_r_o_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     Calculates SNP-specific standard errors for copy number using a
     reference set.

_U_s_a_g_e:

     calculateCnSE(object, referenceSet, epsilon = 0.1)

_A_r_g_u_m_e_n_t_s:

  object: An object of class 'SnpCopyNumberSet' or 'oligoSnpSet'.  

referenceSet: An object of class 'SnpCopyNumberSet' or 'oligoSnpSet'.
          If missing, this function uses the samples in the 'object' to
          estimate across sample standard deviations 

 epsilon: minimum standard error

_D_e_t_a_i_l_s:

     Calculates SNP-specific standard errors from a reference
     distribution as the product of the within copy number standard
     deviation of the sample (test set) and the across samples standard
     deviation from a reference set.  The across samples standard
     deviation is scaled by the median (e.g., across sample sd = across
     sample sd/ median(across sample sd)).

_V_a_l_u_e:

     A matrix of standard errors

_A_u_t_h_o_r(_s):

     R. Scharpf

