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)

