fbat {fbat}R Documentation

Family-Based Association Tests

Description

Family-Based Assoiciation Tests for biallelic markers.

Usage

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

  fbat.default(ped, 
               columns=c("family","pid","father","mother","sex","affected"), 
               model="a", 
               traitMethod=3, 
               traitOffset=0, 
               quiet=TRUE)

Arguments

geneSetObj an object of geneSet.
ped pedigree data frame whose first 6 columns are pid (pedigree id), id (individual id), fid (father id), mid (mother id), sex, aff (affection status). The remaining columns are pairs of marker alleles. Each row corresponds to an individual.
columns names of the first 5 (or 6) columns of ped file. It should be either equal to c("family","pid","father","mother","sex","affect") or equal to c("family","pid","father","mother","sex")
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.

Value

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

Author(s)

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

References

Horvath et al. The family based association test method: computing means and variances for general statistics. Technical report 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.

Examples

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

[Package fbat version 1.0.0 Index]