checkMendelian             package:fbat             R Documentation

_C_h_e_c_k _M_e_n_d_e_l_i_a_n _E_r_r_o_r_s

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

     Check Mendelian errors.

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

     checkMendelian(geneSetObj, quiet = TRUE)

     checkMendelian.default(pedObj, 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

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

_D_e_t_a_i_l_s:

     check the following errors:

     _1 father id = subject id  

     _2 mother id = subject id  

     _3 could not determine if an individual is a parent or a child in a
          family

     _4 inconsistent parental sex in a family

     _5 parental genotypes are not compatible with childrens' genotypes
          in a family

     _6 all childrens' genotypes are missing in a family

     _7 inconsistent sib genotypes in a family

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

     A list with following elements: 

errorFlag: 'errorFlag=1' indicates the occurence of errors;
          'errorFlag=0' indicates no error.

compatibleFlag: 'compatibleFlag=0' indicates the occurence of
          non-compatibility; 'compatibleFlag=1' indicates
          compatibility.

nMerrMarker: A $nMarkers x 1$ vector records the numbers of families
          with non-compatible genotypes, where $nMarkers$ is the number
          of markers.

nMerrFamily: A $nFamily x 1$ vector records the numbers of markers with
          non-compatible genotypes, where $nFamily$ is the number of
          families.

nErrFamilySample: A $nFamily x 1$ vector records the numbers of times
          that father id is equal to subject id or mother id is equal
          to subject id in a family.

_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)
       checkMendelian(CAMP, quiet = TRUE)

