AnnotatedSnpCallSet-class      package:SNPchip      R Documentation

_C_l_a_s_s "_A_n_n_o_t_a_t_e_d_S_n_p_C_a_l_l_S_e_t"

_D_e_s_c_r_i_p_t_i_o_n:

     Container for genotype call data accompanied by SNP annotation

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form
     'new("AnnotatedSnpCallSet", phenoData, experimentData, annotation,
     calls, callsConfidence, snpLocation, chromosomeAnnotation,
     chromosome)'.

_S_l_o_t_s:

     '_c_h_r_o_m_o_s_o_m_e_A_n_n_o_t_a_t_i_o_n': Object of class 'data.frame'

     '_a_s_s_a_y_D_a_t_a': Object of class 'AssayData'

     '_p_h_e_n_o_D_a_t_a': Object of class  'AnnotatedDataFrame'

     '_f_e_a_t_u_r_e_D_a_t_a': Object of class 'AnnotatedDataFrame' contains
          annotation for the SNP's, such as chromosome, physical
          position, and alleles.     

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': Object of class 'MIAME'

     '_a_n_n_o_t_a_t_i_o_n': For 100k chips, "mapping50kHind240",
          "mapping50kXba240" , or "mapping100k".  For 500k chips, mmust
          be "mapping250kNsp" or "mapping250kSty"

     '.___c_l_a_s_s_V_e_r_s_i_o_n__': Object of class 'Versions'

_E_x_t_e_n_d_s:

     Class 'SnpCallSet', directly. Class 'eSet', by class 'SnpCallSet'.
     Class 'VersionedBiobase', by class 'SnpCallSet'. Class
     'Versioned', by class 'SnpCallSet'.

_M_e_t_h_o_d_s:

_N_o_t_e:

_A_u_t_h_o_r(_s):

     Robert Scharpf

_S_e_e _A_l_s_o:

_E_x_a_m_p_l_e_s:

