removeLowQualitySamples     package:beadarraySNP     R Documentation

_Q_u_a_l_i_t_y _c_o_n_t_r_o_l _o_f _S_n_p_S_e_t_I_l_l_u_m_i_n_a _o_b_j_e_c_t_s

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

     Remove samples from a SnpSetIllumina object that show a low
     quality

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

     removeLowQualitySamples(object, min.intensity = 1500, min.gt = 100, subsample = "OPA")

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

  object: 'SnpSetIllumina-class' object

min.intensity: 'numeric'. Samples that show a median intensity below
          this  value in either Red or Green channel are removed

  min.gt: 'numeric'. Samples that have less than this amount of valid 
          genotypes are removed

subsample: factor or column name in 'featureData' slot of 'object'

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

     This function returns an 'SnpSetIllumina' object.

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

     Jan Oosting

_E_x_a_m_p_l_e_s:

       data(chr17.260)
       chr17.260<-removeLowQualitySamples(chr17.260,min.gt=10)

