checkMarkers              package:fbat              R Documentation

_B_a_s_i_c _d_a_t_a _q_u_a_l_i_t_y _c_h_e_c_k_s _f_o_r _m_a_r_k_e_r_s

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

     Basic data quality checks for markers.

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

     checkMarkers(geneSetObj, founderOnly=TRUE, thrsh=0.05, quiet=TRUE)

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

geneSetObj: a 'geneSet' object.

founderOnly: indicates if using only founder info

   thrsh: threshold for Hardy-Weinberg test. If the pvalue of the HW
          test for a marker is greater than 'thrsh', then the marker is
          a good marker.

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

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

     a data frame contains components:  

    Name: marker names.

Position: marker positions.

  ObsHET: marker's observed heterozygosity (i.e., proportion of
          heterozygotes at markes). Missing alleles are excluded in the
          calculation.

 PredHET: marker's predicted heterozygosity (i.e., '2*MAF*(1-MAF)').
          Missing alleles are excluded in the calculation.

  HWpval: pvalues for Hardy-Weinberg test

   pGeno: percentage of non-missing genotypes for markes

     MAF: minor allele frequencies. missing allele are excluded from
          calculation

  Rating: 'Rating[i]=1' means that the $i$-th marker passes HW test (do
          not reject H0 that HW equilibrium holds). 'Rating[i]=0' means
          HW equilibrum does hold for the $i$-th marker.

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

     Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus
     ross.lazarus@channing.harvard.edu

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

       data(CAMP)
       res<-checkMarkers(CAMP)
       print(res)

