calculateQCarray        package:beadarraySNP        R Documentation

_R_e_t_r_i_e_v_e _Q_C _i_n_f_o_r_m_a_t_i_o_n _f_r_o_m _a _S_n_p_S_e_t_I_l_l_u_m_i_n_a _o_b_j_e_c_t

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

     Retrieves QC and identifying information of Illumina Sentrix
     arrays.

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

     calculateQCarray(object, QCobject = NULL, arrayType="Sentrix96")

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

  object: 'SnpSetIllumina' object. Should contain information  of a
          single Sentrix array and a single type of OPA panel

QCobject: 'QCIllumina-class' object: If set the information in the
          object  is amended with data from the SnpSetIllumina object

arrayType: character, see 'arrayType'

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

     Sample summary values are mapped to the physical layout of the 
     Sentrix array using the 'Row' and 'Col' columns of the 'phenoData'
      slot. These will be available when 'read.SnpSetIllumina' is used 
     to create 'SnpSetIllumina' objects.
      Use successive calls to 'calculateQCarray' to process Sentrix
     arrays  with multiple probe panels.

     If data is read using a samplesheet that defines manifest files it
     is possible to handle  data with multiple manifests and/or
     multiple Sentrix arrays

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

     A 'QCIllumina' object, when multiple arrays were combined a list
     of 'QCIllumina' objects

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

     Jan Oosting

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

     'link{QCIllumina-class}', 'link{reportSamplePanelQC}',
     'link{plotQC}'

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

       ## Not run: QC<-calculateQCarray(data.raw1)
       ## Not run: QC<-calculateQCarray(data.raw2,QC)

