detectionCall              package:lumi              R Documentation

_E_s_t_i_m_a_t_e _t_h_e _d_e_t_e_c_t_a_b_l_e _p_r_o_b_e _r_a_t_i_o

_D_e_s_c_r_i_p_t_i_o_n:

     Estimate the detectable probe ratio of each probe, sample or just
     return an AP matrix

_U_s_a_g_e:

     detectionCall(x.lumi, Th = 0.01, type = c('probe', 'sample', 'matrix'))

_A_r_g_u_m_e_n_t_s:

  x.lumi: a LumiBatch object 

      Th: the threshold. By default, when the detection p-value is less
          than 0.01, we suppose it is detectable. For the old version
          of BeadStudio output (version 2 or earlier), the threshold
          will automatically transferred as 1 - Th, because in the old
          format, value close to 1 is suppose to be detectable. 

    type: determine to calculate the detection count by probe or by
          sample 

_V_a_l_u_e:

     If the type is 'probe', then returns the presentCount of each
     probe. If the type is 'sample', then return the detectable probe
     ratio of each sample. If the type is 'matrix', then return the AP
     matrix, in which 'A' represents absent (the detect p-value less
     than threshold) and 'P' represents present.

_A_u_t_h_o_r(_s):

     Pan Du

_S_e_e _A_l_s_o:

     'lumiQ'

_E_x_a_m_p_l_e_s:

     ## load example data
     data(example.lumi)
     ## load example data
     data(example.lumi)

     ## estimate the detect call (percentage of expressed genes) of each sample
     temp <- detectionCall(example.lumi, type='sample')
     print(temp)

     ## estimate the present count of each gene (probe)
     temp <- detectionCall(example.lumi, type='probe')
     hist(temp)

