fbat                  package:fbat                  R Documentation

_F_a_m_i_l_y-_B_a_s_e_d _A_s_s_o_c_i_a_t_i_o_n _T_e_s_t_s

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

     Family-Based Assoiciation Tests for biallelic markers.

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

       fbat(geneSetObj, 
            model="a", 
            traitMethod=3, 
            traitOffset=0, 
            quiet=TRUE)

       fbat.default(pedObj, 
                    model="a", 
                    traitMethod=3, 
                    traitOffset=0, 
                    quiet=TRUE)

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

geneSetObj: an object of 'geneSet'.

  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

   model: Genotype coding method. 'model="d"' means GDOM (dominante)
          coding; 'model="r"' means GREC (recessive) coding;
          'model="g"' means GEN (genotype) coding; 'model="a"' or
          otherwise means GTDT (additive) coding.

traitMethod: Trait coding method. 'traitMethod=1' means 'T=y-offset',
          where 'y' is the trait and 'offset' is an offset. In a .ped
          file, 'y=2' if affected; 'y=1' if unaffected; and 'y=0' if
          unknown. 'traitMethod=2' means 'T=1' if affected, 'T=0'
          otherwise.

traitOffset: Offset if 'traitMethod=1'.

   quiet: Print some intermediate results if 'quiet=FALSE'.

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

statPvalue: A 'm' by 3 matrix with the 3 columns: test statistics,
          degree of freedom and pvalues, where 'm' is the number of
          markers.

  S.list: A list of S scores for markers.

 ES.list: A list of expected S scores for markers.

CovS.list: A list of covariance matrix of S scores for markers.

alleles.list: A list of alleles for markers

familySize: size of nuclear families

flagMarkers: A vector of flags. 'flagMarkers[i]=1' if for marker 'i',
          all children genotypes in all families are missing. Otherwise
          'flagMarkers[i]=0'.

numInfoFamily: number of informative families at each 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

_R_e_f_e_r_e_n_c_e_s:

     Horvath et al.  The family based association test method:
     computing means and variances for general statistics. _Technical
     report <URL:
     http://www.biostat.harvard.edu/~fbat/fbattechreport.ps>._

     Rabinowitz and Laird (2000). A Unified Approach to Adjusting
     Association Tests for Population Admixture with Arbitrary Pedigree
     Structure and Arbitrary Missing Marker Information. _Human
     Heredity *50*:211-223._  

     Laird et al. (2000). Implementing a Unified Approach to
     Family-Based Tests of Association. _Genetic Epidemiology *19(Suppl
     1)*:S36-S42._

     Schaid (1996). General Score Tests for Associations of Genetic
     Markers With Disease Using Cases and Their Parents. _Genetic
     Epidemiology *13*:423-449._

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

       data(CAMP)
       tmp<-fbat(CAMP)
       summaryPvalue(tmp)

