genotypeSummary         package:GeneticsBase         R Documentation

_p_r_i_n_t _t_h_e _s_u_m_m_a_r_y _o_f _g_e_n_o_t_y_p_e_s _s_o_r_t_e_d _b_y _m_a_r_k_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     print the summary of genotypes sorted by markers

_U_s_a_g_e:

     genotypeSummary(object, 
                     by = NULL, 
                     confidence = 0.95, 
                     alpha = 1 - confidence, 
                     show = TRUE, 
                     HWE.method = c("simulate", "exact"), 
                     simulate.p.value = TRUE, 
                     B = 10000, 
                     verbose = FALSE, 
                     includeOverall = FALSE, 
                     omitRepeats = TRUE, 
                     founderOnly = FALSE, 
                     ...)

_A_r_g_u_m_e_n_t_s:

  object: geneSet object 

      by: optional column name, by which the summary is desired.
          Default is NULL. 

confidence: confidence intervals of Genotype frequencies within each
          marker (default is 95%) 

   alpha: Type -1 error rate = (1- confidence) 

    show: No longer used 

HWE.method: Method to be used for Hardy-Weinberg Equilibrium
          Significance Test, exact or simulate 

simulate.p.value: No longer used 

       B: No longer used 

 verbose: No longer used

includeOverall: logical value (TRUE/FALSE) indicating whether overall
          summary is also needed, default = FALSE 

omitRepeats: logical value (TRUE/FALSE) indicating whether Gene name
          and marker name should be printed repeatedly for each
          Genotype, default = TRUE 

founderOnly: logical value (TRUE/FALSE) indicating whether founder
          information should be extracted from the geneSet object,
          default = FALSE 

     ...: any further arguments to print

_D_e_t_a_i_l_s:

     We can print the genotypeSummary on screen, or save in .html
     format or .tex format

_A_u_t_h_o_r(_s):

     Nitin Jain nitin.jain@pfizer.com

_E_x_a_m_p_l_e_s:

     library(GeneticsBase)
     data(CAMP)

     temp <- genotypeSummary(CAMP)

     print(temp)
     txt(temp, filename="genotypeSummary.txt")
     html(temp, filename="genotypeSummary.html")
     latex(temp, filename="genotypeSummary.tex")

