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)
     checkMarkers.default(pedObj, founderOnly=TRUE, thrsh=0.05, quiet=TRUE)

_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

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,  Gregory Warnes
     warnes@bst.rochester.edu, Nitin Jain nitin.jain@pfizer.com

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

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

