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
_m_e_t_h_o_d _o_u_t_p_u_t_s _a_n_d _a_l_l_i_e_d _o_b_j_e_c_t_s

_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")

