pedHardyWeinberg            package:fbat            R Documentation

_T_e_s_t _H_a_r_d_y-_W_e_i_n_b_e_r_g _e_q_u_i_l_i_b_r_i_u_m _f_o_r _e_a_c_h _m_a_r_k_e_r _b_a_s_e_d _o_n _p_a_r_e_n_t_a_l _d_a_t_a

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

     Test Hardy-Weinberg equilibrium for each marker based on parental
     data.

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

     pedHardyWeinberg(geneSetObj, threshold=3, founderOnly=TRUE, quiet=FALSE)

     pedHardyWeinberg.default(pedObj, 
               threshold=3, founderOnly=TRUE, quiet=FALSE)

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

geneSetObj: a 'geneSet' object.

  pedObj: a list with five elements: 'ped', 'columns', 'markerNames',
          'Position', and 'filename'. 'ped' is a pedigree data frame
          whose first 6 columns are family (pedigree id), pid (patient
          id), father (father id), mother (mother id), sex, affected
          (affection status). The remaining columns are pairs of marker
          alleles. Each row corresponds to an individual; 'columns' are
          the names of the first 5 (or 6) columns of ped file. It
          should be either equal to 
          c("family","pid","father","mother","sex","affected") or equal
          to c("family","pid","father","mother","sex"); 'founderOnly'
          indicates if using only founder info; 'markerNames' is a
          vector of marker names; 'Position' is a vector of marker
          positions; 'fileName' is the pedigree file name

threshold: a threshold to check if expected frequencies of genotypes
          are too small.

founderOnly: indicates if using only founder info

   quiet: print intermediate results if 'quiet=FALSE'.

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

  resMat: A matrix records the following quantities for all markers
          (rows correspond to markers): 'nInfoInd' (number of
          informative individuals, i.e. individuals whose genotypes
          contain no missing alleles for the specified marker),
          'nGenotype' (number of possible genotypes), 'nHET' (number of
          heterozygous genotypes), 'nHOM' (number of homozygous
          genotypes), 'nAllele' (number of alleles), 'nMissing' (number
          of missing alleles), 'chi2' (chi square test statistic), 'df'
          (degree of freedom of the chi square test statistic under
          H0), 'p-value' (pvalue of the test).

genotype: A list of possible genotypes and their frequencies for all
          markers.

nGenotype.vec: A vector of numbers of possible genotypes for all
          markers.

   piVec: Allele frequencies for all markers.

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

     Weiliang Qiu stwxq@channing.harvard.edu,  Ross Lazarus
     ross.lazarus@channing.harvard.edu,  Gregory Warnes
     warnes@bst.rochester.edu, Nitin Jain nitin.jain@pfizer.com

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

       data(CAMP)
       res<-pedHardyWeinberg(CAMP)
       viewHW(res, "m709")
       viewHW(res, "m654")
       viewHW(res, "m47")
       viewHW(res, "p46")
       viewHW(res, "p79")
       viewHW(res, "p252")
       viewHW(res, "p491")
       viewHW(res, "p523")

