createCNSummary         package:beadarraySNP         R Documentation

_S_u_m_m_a_r_i_z_a_t_i_o_n _o_f _C_o_p_y _n_u_m_b_e_r _s_t_a_t_e_s

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

     Create a summary object of the genomic copy number states in a
     sample of segmented data

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

     createCNSummary(object, sample, dnaIndex=1, subsample = "OPA")

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

  object: SNPSetIllumina object after segmentation 'segmentate' 

  sample: SampleName or index of the sample for which to create the
          summary

dnaIndex: Measured DNA index of the sample

subsample: factor or column name in 'featureData' slot 

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

     The segments within a sample are assigned a copy number value.
     When the 'inferred' slot  in 'assayData' is empty, all segments
     will be set to 2. Otherwise the values are recovered from the
     'inferred' slot. Gender is taken into account for the sex
     chromosomes.

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

     list with the following elements 

dnaIndex : same as parameter dnaIndex

CN.total.nrm: Total expected copynumber for a 'normal' specimen ~
          2*featurecount

  states: data.frame with columns 'opa, count ,intensity, copynumber'

     This list can be used as the 'cn.sum' argument for
     'plotGoldenGate4OPA, alterCN,  getDNAindex' and 'setRealCN'

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

     Jan Oosting

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

     'segmentate, alterCN, plotGoldenGate4OPA '

