gwSnpScreenResult-class        package:GGBase        R Documentation

_C_l_a_s_s "_g_w_S_n_p_S_c_r_e_e_n_R_e_s_u_l_t" - _c_o_n_t_a_i_n_e_r_s _f_o_r _G_G_t_o_o_l_s _g_w_S_n_p_S_c_r_e_e_n
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_D_e_s_c_r_i_p_t_i_o_n:

     Class "gwSnpScreenResult" - container for GGtools gwSnpScreen
     method outputs and allied objects

_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("gwSnpScreenResult", ...)'. These will be primarily lists of
     inference tables (snps are rows, columns are statistics and
     p-values).  Additional slots manage analysis metadata.

     gwSnpScreenResult is intended for genome-wide analysis of
     expression for a single gene.

     cwSnpScreenResult is intended for the restriction to a single
     chromosome.

     multiGwSnpScreenResult is intended for analyses with multiple
     genes.

     Because the vast majority of tests are uninformative, early
     filtering is important for managing object sizes. Instances of
     filteredGwSnpScreenResult and filteredMultiGwSnpScreenResult are
     created when a snpdepth parameter is used with gwSnpTests.

_S_l_o_t_s:


     '._D_a_t_a': Object of class '"list"' containing inference tables
          (snps are rows, columns are statistics and p-values) 

     '_g_e_n_e': Object of class '"character"' typically the HUGO symbol of
          the gene analyzed 

     '_p_s_i_d': Object of class '"character"' the feature identifier of
          the associated microarray 

     '_a_n_n_o_t_a_t_i_o_n': Object of class '"character"' vector of relevant
          annotation package identifier names 

     '_f_o_r_m_u_l_a': Object of class '"formula"' the formula used to fit the
          model relating expression to genotype 

_E_x_t_e_n_d_s:

     Class '"list"', from data part. Class '"vector"', by class "list",
     distance 2. Class 'AssayData', by class "list",  distance 2.

_M_e_t_h_o_d_s:

     plot and show

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

     VJ Carey <stvjc@channing.harvard.edu>

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

     showClass("gwSnpScreenResult")
     showClass("cwSnpScreenResult")

