calculateCopyNumber       package:oligoClasses       R Documentation

_C_a_l_c_u_l_a_t_e_s _c_o_p_y _n_u_m_b_e_r _a_s _t_h_e _a_v_e_r_a_g_e _o_f _S_N_P-_l_e_v_e_l _s_u_m_m_a_r_i_e_s _f_r_o_m
_t_h_e _A _a_n_d _B _a_l_l_e_l_e_s

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

     Calculates copy number as the average of SNP-level summaries from
     the A and B alleles from an object of class 'SnpCallSetPlus'

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

     calculateCopyNumber(object, ...)

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

  object: an instance of 'SnpCallSetPlus'

     ...: Not implemented

_D_e_t_a_i_l_s:

     The average A (and B) allele intensities for each SNP is centered
     by the median intensity across samples (should have a reasonable
     (e.g., > 10) samples).  Addtionally, we assume that the median
     intensity across all samples for autosomes should be the same for
     homozygous genotypes and heterozygous geneotypes.  The resulting
     intensities are then recentered at 2 copies (for autosomes), 1 for
     the male X chromosome, 2 for the female X, etc.  We assume that
     for a given SNP, the median copy number is normal. If this is not
     likely to be the case, alternative approaches should be explored.

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

     A matrix of copy number intensities.

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

     R. Scharpf

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

     'SnpCallSetPlus-class'

