getA                  package:oligo                  R Documentation

_C_o_m_p_u_t_e _a_v_e_r_a_g_e _l_o_g-_i_n_t_e_n_s_i_t_i_e_s / _l_o_g-_r_a_t_i_o_s

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

     Methods to compute average log-intensities and log-ratios across
     alleles, within strand.

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

     getA(obj)
     getM(obj)

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

     obj: 'SnpQSet' object.

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

     SNPRMA summarizes the SNP information into 4 quantities
     (log2-scale):

_a_n_t_i_s_e_n_s_e_T_h_e_t_a_A antisense allele A

_a_n_t_i_s_e_n_s_e_T_h_e_t_a_B antisense allele B

_s_e_n_s_e_T_h_e_t_a_A sense allele A

_s_e_n_s_e_T_h_a_t_a_B sense allele B

     The average log-intensities are given by:
     '(antisenseThetaA+antisenseThetaB)/2' and
     '(senseThetaA+senseThetaB)/2'.

     The average log-ratios are given by:
     'antisenseThetaA-antisenseThetaB' and 'senseThetaA-senseThetaB'.

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

     A 3-dimensional array (SNP's x Samples x Strand) with the
     requested measure.

     If a Genomewide array (like Affy SNP 6.0) is used, the strand
     dimension described above is dropped.

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

     'snprma'

